Demo of animation jank with AnimatedContainer with Theme.of(context) color used in color property. It causes jank on Web CanvasKit master builds, but not on Beta channel.

main.dart

// MIT License
// Copyright 2020 Mike Rydstrom
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
// IN THE SOFTWARE.

import 'package:flutter/material.dart';
import 'package:flutter/services.dart';

// ****************************************************************************
// Const and finals for setup and theme

const double kEdgePadding = 16.0;
const double kMaxContentWidth = 1200.0;
const double kExpandWidth = 250;
const double kShrinkWidth = 70;
const double kMinCardWidth = 200;
const int kMaxCards = 200;

// Custom Eden palette
// Color sources: https://www.w3schools.com/colors/colors_2019.asp
const Color lightPrimary = Color(0xFF264E36); // Eden 23%
const Color lightPrimaryVariant = Color(0xFF224430); // Eden 20%
const Color lightSecondary = Color(0xFF797b3a); // Guacamole 35%
const Color lightSecondaryVariant = Color(0xFF555729); // Guacamole 25%

final Color lightCanvas = Color.alphaBlend(
    lightPrimary.withAlpha((256 * 0.07).toInt()), Colors.white);

const Color darkPrimary = Color(0xFF59a678); // Eden light 50%
const Color darkPrimaryVariant = Color(0xFF478560); // Eden light 40%
const Color darkSecondary = Color(0xFFd5d6a8); // Guacamole 75%
const Color darkSecondaryVariant = Color(0xFFbbbe74); // Guacamole 60%

final Color darkCanvas = Color.alphaBlend(
    darkPrimary.withAlpha((256 * 0.12).toInt()), const Color(0xFF121212));

const ColorScheme lightScheme = ColorScheme.light(
  primary: lightPrimary,
  primaryVariant: lightPrimaryVariant,
  secondary: lightSecondary,
  secondaryVariant: lightSecondaryVariant,
);

const ColorScheme darkScheme = ColorScheme.dark(
  primary: darkPrimary,
  primaryVariant: darkPrimaryVariant,
  secondary: darkSecondary,
  secondaryVariant: darkSecondaryVariant,
);

final ThemeData lightTheme = ThemeData.from(colorScheme: lightScheme).copyWith(
  canvasColor: lightCanvas,
  toggleableActiveColor: lightScheme.secondary,
  buttonTheme: const ButtonThemeData(
    colorScheme: lightScheme,
    textTheme: ButtonTextTheme.primary,
  ),
);

final ThemeData darkTheme = ThemeData.from(colorScheme: darkScheme).copyWith(
  canvasColor: darkCanvas,
  toggleableActiveColor: darkScheme.secondary,
  buttonTheme: const ButtonThemeData(
    colorScheme: darkScheme,
    textTheme: ButtonTextTheme.primary,
  ),
);

// ****************************************************************************

void main() {
  runApp(MyApp());
}

class MyApp extends StatefulWidget {
  @override
  _MyAppState createState() => _MyAppState();
}

class _MyAppState extends State<MyApp> {
  bool isDarkMode;

  @override
  void initState() {
    isDarkMode = false;
    super.initState();
  }

  @override
  Widget build(BuildContext context) {
    final ThemeData theme = Theme.of(context);

    SystemChrome.setSystemUIOverlayStyle(
      SystemUiOverlayStyle(
        statusBarColor: Colors.transparent,
        statusBarIconBrightness: Theme.of(context).brightness,
        systemNavigationBarColor: theme.scaffoldBackgroundColor,
        systemNavigationBarIconBrightness: theme.brightness == Brightness.light
            ? Brightness.dark
            : Brightness.light,
      ),
    );

    return MaterialApp(
      title: 'Issue Discovery',
      debugShowCheckedModeBanner: false,
      theme: lightTheme,
      darkTheme: darkTheme,
      themeMode: isDarkMode ? ThemeMode.dark : ThemeMode.light,
      home: DemoPage(
        title: 'Issue Discovery',
        setDarkMode: (bool value) {
          setState(() {
            isDarkMode = value;
          });
        },
      ),
    );
  }
}

class DemoPage extends StatefulWidget {
  const DemoPage({
    Key key,
    this.title,
    this.setDarkMode,
  }) : super(key: key);
  final String title;
  final ValueChanged<bool> setDarkMode;

  @override
  _DemoPageState createState() => _DemoPageState();
}

class _DemoPageState extends State<DemoPage> {
  double width;
  bool isSidePanelExpanded;
  bool showSidePanel;
  bool isDarkMode;
  bool problemOn;

  @override
  void initState() {
    width = kExpandWidth;
    isSidePanelExpanded = true;
    showSidePanel = true;
    isDarkMode = false;
    problemOn = true;
    super.initState();
  }

  @override
  Widget build(BuildContext context) {
    final MediaQueryData media = MediaQuery.of(context);
    final double topPadding = media.padding.top;
    final double bottomPadding = media.padding.bottom;
    final Size size = media.size;
    final ThemeData theme = Theme.of(context);
    final TextTheme textTheme = theme.textTheme;
    final TextStyle headline6 = textTheme.headline6;
    final TextStyle caption = theme.primaryTextTheme.caption;

    return Row(
      children: <Widget>[
        ConstrainedBox(
          constraints: const BoxConstraints(maxWidth: kExpandWidth),
          child: Material(
            elevation: 0,
            child: AnimatedContainer(
              //
              // ISSUE CAUSING LINE
              // The line causing the issue on Web master CanvasKit build was
              // not needed for the use case on the AnimatedContainer below.
              // It was a remnant from older revision.
              // In this demo the problematic color assignment can be
              // toggled on and/off to see its effect.
              //
              // It is not so surprising that this may cause problems, what is
              // curious is that it has hardly any impact on any Android ir
              // Windows target, but on Web CanvasKit on master channel it
              // breaks and janks badly and causes very surprising behavior.
              //
              color: problemOn ? Theme.of(context).canvasColor : null,
              //
              //
              duration: const Duration(milliseconds: 300),
              width: width,
              child: SideContent(
                isVisible: showSidePanel,
                menuWidth: kExpandWidth,
              ),
            ),
          ),
        ),
        Expanded(
          child: Scaffold(
            extendBodyBehindAppBar: true,
            extendBody: true,
            appBar: AppBar(
              title: Row(
                children: <Widget>[
                  Text(widget.title),
                  // Show canvas size in the app bar
                  Expanded(
                    child: Text(
                      " W:${size.width.round()} H:${size.height.round()}",
                      style: caption,
                      textAlign: TextAlign.right,
                    ),
                  ),
                ],
              ),
              centerTitle: false,
              elevation: 0,
              backgroundColor: Colors.transparent,
              // Gradient partially transparent AppBar
              flexibleSpace: Container(
                decoration: BoxDecoration(
                  border: Border(
                    bottom: BorderSide(color: Theme.of(context).dividerColor),
                  ),
                  gradient: LinearGradient(
                    begin: AlignmentDirectional.centerStart,
                    end: AlignmentDirectional.centerEnd,
                    colors: <Color>[
                      theme.primaryColor,
                      theme.primaryColor.withOpacity(0.7),
                    ],
                  ),
                ),
                child: null,
              ),
            ),
            body: Scrollbar(
              child: Center(
                child: ConstrainedBox(
                  constraints: const BoxConstraints(maxWidth: kMaxContentWidth),
                  child: ListView(
                    padding: EdgeInsets.fromLTRB(
                      kEdgePadding,
                      topPadding + kToolbarHeight + kEdgePadding,
                      kEdgePadding,
                      kEdgePadding + bottomPadding,
                    ),
                    children: <Widget>[
                      Text(
                        'Animation issue on CanvasKit',
                        style: textTheme.headline4,
                      ),
                      const Divider(),
                      Text('Issue 1', style: headline6),
                      const Text(
                        'An AnimatedContainer that move content on the page has janky '
                        'size animation when built for CanvasKit, it is like there is no animation. '
                        'This can be demonstrated by toggling the side panel width below or '
                        'hiding it completely. This issue can only be observed '
                        'when the application is built for CanvasKit with master channel. If built '
                        'for WEB CanvasKit on Beta, it is not as visible. When built '
                        'built for a device on stable or even Windows with master, it is not visible. ',
                      ),
                      SwitchListTile.adaptive(
                        title: const Text(
                          'Expanded and collapse the side panel',
                        ),
                        subtitle: const Text(
                          'Turn OFF for a narrow side panel',
                        ),
                        value: isSidePanelExpanded,
                        onChanged: (bool value) {
                          setState(() {
                            isSidePanelExpanded = value;
                            if (showSidePanel) {
                              if (isSidePanelExpanded) {
                                width = kExpandWidth;
                              } else {
                                width = kShrinkWidth;
                              }
                            } else {
                              width = 0;
                            }
                          });
                        },
                      ),
                      SwitchListTile.adaptive(
                        title: const Text(
                          'Show and hide the side panel',
                        ),
                        subtitle: const Text(
                            'Turn OFF to hide the side panel completely'),
                        value: showSidePanel,
                        onChanged: (bool value) {
                          setState(() {
                            showSidePanel = value;
                            if (showSidePanel) {
                              if (isSidePanelExpanded) {
                                width = kExpandWidth;
                              } else {
                                width = kShrinkWidth;
                              }
                            } else {
                              width = 0;
                            }
                          });
                        },
                      ),
                      //
                      // Change theme
                      //
                      const Divider(),
                      Text('Issue 2', style: headline6),
                      const Text(
                          'Theme change animations in the AnimatedContainer are '
                          'janky and may not always complete.'),
                      SwitchListTile.adaptive(
                        title: const Text(
                          'Change theme mode',
                        ),
                        value: isDarkMode,
                        onChanged: (bool value) {
                          setState(() {
                            isDarkMode = value;
                            widget.setDarkMode(isDarkMode);
                          });
                        },
                      ),
                      const Divider(),
                      Text('Cause of issue', style: headline6),
                      const Text(
                          'During the creation of this demo, the point causing '
                          'the issue was found. Setting a theme based color on '
                          'the AnimatedContainer handling the expanding '
                          'side panel causes the yank and the issue on the '
                          'theme change.'),
                      SwitchListTile.adaptive(
                        title: const Text(
                          'Issue ON/OFF',
                        ),
                        subtitle: const Text(
                          'Turn off to remove the "Theme.of" color '
                          'from the AnimatedContainer handling the side '
                          'panel width, will also remove the issue!',
                        ),
                        value: problemOn,
                        onChanged: (bool value) {
                          setState(() {
                            problemOn = value;
                          });
                        },
                      ),
                      //
                      // Source code location info
                      //
                      const Divider(),
                      Text('Source code location of this demo',
                          style: headline6),
                      const SelectableText(
                          'https://gist.github.com/rydmike/2e8e6a4cc9126dbe6f95e81e674f6d6b'),
                      const Divider(),
                      //
                      // A Card GridView with responsive column amount. This is
                      // just here to put some content on the page to stress it
                      // a bit during resizing and scaling.
                      //
                      const SizedBox(height: kEdgePadding),
                      Text('Colorful cards in a responsive GridView',
                          style: headline6),
                      LayoutBuilder(
                        builder:
                            (BuildContext context, BoxConstraints constraint) {
                          final int nrOfColumns =
                              (constraint.maxWidth.toInt()) ~/
                                  kMinCardWidth.toInt();
                          return GridView.builder(
                            padding: const EdgeInsets.all(kEdgePadding),
                            shrinkWrap: true,
                            primary: false,
                            gridDelegate:
                                SliverGridDelegateWithFixedCrossAxisCount(
                              crossAxisCount:
                                  nrOfColumns == 0 ? 1 : nrOfColumns,
                              mainAxisSpacing: kEdgePadding,
                              crossAxisSpacing: kEdgePadding,
                              childAspectRatio: 1.4,
                            ),
                            itemCount: kMaxCards,
                            itemBuilder: (_, int index) => Card(
                              elevation: 3,
                              child: GridItem(
                                title: 'Card ${index + 1}',
                                color: Colors.primaries[
                                        index % Colors.primaries.length][
                                    Theme.of(context).brightness ==
                                            Brightness.light
                                        ? 600
                                        : 300],
                              ),
                            ),
                          );
                        },
                      )
                    ],
                  ),
                ),
              ),
            ),
          ),
        ),
      ],
    );
  }
}

// This hole thing could just have been a container and we would still have
// the same issue, but Ok at least it is a bit more representative of the use
// case where it was found like this.

class SideContent extends StatefulWidget {
  const SideContent({
    Key key,
    this.isVisible,
    this.menuWidth,
  }) : super(key: key);
  final bool isVisible;
  final double menuWidth;

  @override
  _SideContentState createState() => _SideContentState();
}

class _SideContentState extends State<SideContent> {
  int selectedItem;

  @override
  void initState() {
    selectedItem = 2;
    super.initState();
  }

  @override
  Widget build(BuildContext context) {
    return LayoutBuilder(
      builder: (BuildContext context, BoxConstraints size) {
        return OverflowBox(
          alignment: AlignmentDirectional.topStart,
          minWidth: 0.0,
          maxWidth: widget.menuWidth,
          child: Column(
            crossAxisAlignment: CrossAxisAlignment.start,
            children: <Widget>[
              AppBar(
                title: const Text('Side panel'),
                leading: ConstrainedBox(
                  constraints: const BoxConstraints.tightFor(width: 56),
                  child: IconButton(
                    icon: const Icon(Icons.adjust),
                    onPressed: () {},
                  ),
                ),
                elevation: 0,
                flexibleSpace: Container(
                  height: kToolbarHeight,
                  decoration: BoxDecoration(
                    border: Border(
                      bottom: BorderSide(color: Theme.of(context).dividerColor),
                    ),
                  ),
                  child: null,
                ),
              ),
              Expanded(
                child: Container(
                  width: size.maxWidth,
                  decoration: BoxDecoration(
                    border: widget.isVisible
                        ? BorderDirectional(
                            end: BorderSide(
                              color: Theme.of(context).dividerColor,
                            ),
                          )
                        : null,
                  ),
                  child: ListView(
                    padding:
                        const EdgeInsets.only(), //  Removes all edge insets
                    children: <Widget>[
                      for (int i = 0; i < 8; i++)
                        Column(
                          crossAxisAlignment: CrossAxisAlignment.start,
                          children: <Widget>[
                            SideItem(
                              width: size.maxWidth,
                              menuWidth: widget.menuWidth,
                              onTap: () {
                                setState(() {
                                  selectedItem = i;
                                });
                              },
                              selected: selectedItem == i,
                              icon: Icons.account_circle,
                              label: "This is item $i",
                              showDivider: (i % 3 == 0) && i != 0,
                            ),
                          ],
                        ),
                    ],
                  ),
                ),
              ),
            ],
          ),
        );
      },
    );
  }
}

// Totally don't need this either for the issue demo, but since I added it
// while looking for the cause, I't can stay to make the demo case a bit more
// realistic looking

class SideItem extends StatelessWidget {
  const SideItem({
    Key key,
    this.width,
    this.menuWidth,
    this.onTap,
    this.selected = false,
    this.icon,
    this.label,
    this.showDivider = false,
  }) : super(key: key);

  final double width;
  final double menuWidth;
  final VoidCallback onTap;
  final bool selected;
  final IconData icon;
  final String label;
  final bool showDivider;

  @override
  Widget build(BuildContext context) {
    if (width < 5) {
      return const SizedBox.shrink();
    } else {
      return Column(
        crossAxisAlignment: CrossAxisAlignment.start,
        children: <Widget>[
          if (showDivider) const Divider(thickness: 1, height: 1),
          Padding(
            padding: const EdgeInsetsDirectional.fromSTEB(0, 2, 5, 2),
            child: Material(
              clipBehavior: Clip.antiAlias,
              borderRadius: const BorderRadius.only(
                topRight: Radius.circular(50 / 2.0),
                bottomRight: Radius.circular(50 / 2.0),
              ),
              color: selected
                  ? Theme.of(context).colorScheme.primary.withAlpha(0x3d)
                  : Colors.transparent,
              child: InkWell(
                onTap: onTap,
                child: Container(
                  height: 50,
                  width: width - 5,
                  child: OverflowBox(
                    alignment: AlignmentDirectional.topStart,
                    minWidth: 0.0,
                    maxWidth: menuWidth,
                    child: Row(
                      crossAxisAlignment: CrossAxisAlignment.center,
                      children: <Widget>[
                        ConstrainedBox(
                          constraints: const BoxConstraints.tightFor(
                              width: 56, height: 56),
                          child: Icon(icon),
                        ),
                        if (width < kShrinkWidth + 10)
                          const SizedBox.shrink()
                        else
                          Text(label)
                      ],
                    ),
                  ),
                ),
              ),
            ),
          ),
        ],
      );
    }
  }
}

// The grid items for the gridview with cards, not relevant for this case,
// just in the demo app as filler to stress it a bit more during resizing.

class GridItem extends StatelessWidget {
  const GridItem({Key key, this.title, this.color}) : super(key: key);

  final String title;
  final Color color;

  @override
  Widget build(BuildContext context) {
    final Color textColor =
        ThemeData.estimateBrightnessForColor(color) == Brightness.light
            ? Colors.black87
            : Colors.white70;
    return Container(
      color: color,
      padding: const EdgeInsets.all(10),
      child: Column(
        mainAxisAlignment: MainAxisAlignment.center,
        children: <Widget>[
          Text(
            title,
            style: TextStyle(
              color: textColor,
              fontSize: 18,
            ),
          ),
          Icon(Icons.apps, color: textColor),
        ],
      ),
    );
  }
}

For more info on the issue and what lead up to detection of its cause, please refer to this case:
flutter/flutter#63740

Added a MIT license to the file in case somebody wants to use this for something as it got pretty elaborate for a simple issue demo and there might be parts in it that somebody finds useful.