Fixed Sample code showing checkmark on UICollectionViewCell. This is fixed version of https://gist.github.com/hahnah/2b3f0f373562e1cdc80740b7e0ff5d47

CollectionViewController.swift

import UIKit

class CollectionViewController: UIViewController, UICollectionViewDelegate, UICollectionViewDataSource {
    
    var collectionView : UICollectionView!
    var toolbar: UIToolbar?
    
    override func viewDidLoad() {
        super.viewDidLoad()
        
        let viewWidth = self.view.frame.width
        let viewHeight = self.view.frame.height
        
        let collectionFrame = CGRect(x: 0, y: 0, width: viewWidth, height: viewHeight)
        
        // CollectionViewのレイアウトを生成.
        let layout = UICollectionViewFlowLayout()
        // Cell間の最小サイズ
        layout.minimumInteritemSpacing = 4
        // 行間の最小サイズ
        layout.minimumLineSpacing = 4
        // Cellのマージン.
        layout.sectionInset = UIEdgeInsets.zero
        //layout.sectionInset = UIEdgeInsetsMake(16, 16, 16, 16)
        // セクションのヘッダーサイズ
        layout.headerReferenceSize = CGSize(width:0,height:0)
        // Cellサイズを適当に決める
        layout.itemSize = CGSize(width: (viewWidth - layout.minimumInteritemSpacing - 8) / 3, height: (viewWidth - layout.minimumLineSpacing - 8) / 3)
        
        // CollectionViewを生成.
        collectionView = UICollectionView(frame: collectionFrame, collectionViewLayout: layout)
        // Cell に使われるクラスとして CustomCell を登録
        collectionView.register(CustomCell.self, forCellWithReuseIdentifier: "MyCell")
        
        collectionView.delegate = self
        collectionView.dataSource = self
        self.view.addSubview(collectionView)
        
        // 複数選択を許可
        self.collectionView.allowsMultipleSelection = true
    }
    
    // Cell の総数
    func collectionView(_ collectionView: UICollectionView, numberOfItemsInSection section: Int) -> Int {
        return 36
    }
    
    // Cell に値を設定する
    func collectionView(_ collectionView: UICollectionView, cellForItemAt indexPath: IndexPath) -> UICollectionViewCell {
        let cell : CustomCell = collectionView.dequeueReusableCell(withReuseIdentifier: "MyCell", for: indexPath) as! CustomCell
        cell.contentView.backgroundColor = UIColor.yellow
        
        // 古い subview を削除
        cell.contentView.subviews.forEach { subview in
            subview.removeFromSuperview()
        }
        
        // checkmarkをつけ直す
        if CustomCell.hasCellAppearedInThePast(selectedItemAt: indexPath) {
            if CustomCell.shouldCellBeMarked(selectedItemAt: indexPath) {
                cell.mark(selectedItemAt: indexPath)
            } else {
                cell.unmark(deselectedItemAt: indexPath)
            }
        }
        
        return cell
    }
    
    // Cell がタップで選択されたときに呼ばれる
    func collectionView(_ collectionView: UICollectionView, didSelectItemAt indexPath: IndexPath) {
        guard let cell: CustomCell = collectionView.cellForItem(at: indexPath) as? CustomCell else { return }
        if self.collectionView.allowsMultipleSelection {
            cell.mark(selectedItemAt: indexPath)
        }
    }
    
    // Cell がタップで選択解除されたときに呼ばれる
    func collectionView(_ collectionView: UICollectionView, didDeselectItemAt indexPath: IndexPath) {
        guard let cell: CustomCell = collectionView.cellForItem(at: indexPath) as? CustomCell else { return }
        if self.collectionView.allowsMultipleSelection {
            cell.unmark(deselectedItemAt: indexPath)
        }
    }
    
}

CustomCell.swift

import UIKit

class CustomCell: UICollectionViewCell {
    let checkmarkImage: UIImage = UIImage(named: "checkmark")!
    var checkmarkView: UIImageView!
    
    static var allCells: [CustomCell] = []
    
    // 全 Cell のチェックマークの有無を記憶
    static var checkmarkStates: [Bool] = []
    
    // 全チェックマークを消す
    static func clearAllCheckmarks() -> Void {
        allCells.filter { cell in cell.isMarked } .forEach { cell in
            cell.isMarked = false
        }
        checkmarkStates = checkmarkStates.map { _ in
            return false
        }
    }
    
    // indexPath.row 番目の Cell が既に作成されているかどうか判定
    static func hasCellAppearedInThePast(selectedItemAt indexPath: IndexPath) -> Bool {
        if indexPath.row + 1 <= checkmarkStates.count {
            return true
        } else {
            return false
        }
    }
    
    // indexPath.row 番目の Cell にチェックマークがついているか判定
    static func shouldCellBeMarked(selectedItemAt indexPath: IndexPath) -> Bool {
        if checkmarkStates[indexPath.row] {
            return true
        } else {
            return false
        }
    }
    
    // チェックマーク有無
    private var isMarked: Bool = false {
        didSet {
            if isMarked {
                self.contentView.addSubview(self.checkmarkView!)
            } else {
                self.checkmarkView?.removeFromSuperview()
            }
        }
    }
    
    // チェックマークをつける
    func mark(selectedItemAt indexPath: IndexPath) -> Void {
        self.isMarked = true
        CustomCell.checkmarkStates[indexPath.row] = true
    }
    
    // チェックマークを消す
    func unmark(deselectedItemAt indexPath: IndexPath) -> Void {
        self.isMarked = false
        CustomCell.checkmarkStates[indexPath.row] = false
    }
    
    override init(frame: CGRect) {
        super.init(frame: frame)
        self.checkmarkView = UIImageView(image: self.checkmarkImage)
        CustomCell.checkmarkStates.append(false)
        CustomCell.allCells.append(self)
    }
    
    required init?(coder aDecoder: NSCoder) {
        fatalError("init(coder:) has not been implemented")
    }
    
}

ExtendedCollectionViewController.swift

import UIKit

class ExtendedCollectionViewController: UIViewController, UICollectionViewDelegate, UICollectionViewDataSource {
    
    var collectionView : UICollectionView!
    var toolbar: UIToolbar?
    
    override func viewDidLoad() {
        super.viewDidLoad()
        
        let viewWidth = self.view.frame.width
        let viewHeight = self.view.frame.height
        
        let collectionFrame = CGRect(x: 0, y: 0, width: viewWidth, height: viewHeight)
        
        // CollectionViewのレイアウトを生成.
        let layout = UICollectionViewFlowLayout()
        // Cell間の最小サイズ
        layout.minimumInteritemSpacing = 4
        // 行間の最小サイズ
        layout.minimumLineSpacing = 4
        // Cellのマージン.
        layout.sectionInset = UIEdgeInsets.zero
        //layout.sectionInset = UIEdgeInsetsMake(16, 16, 16, 16)
        // セクションのヘッダーサイズ
        layout.headerReferenceSize = CGSize(width:0,height:0)
        // Cellサイズを適当に決める
        layout.itemSize = CGSize(width: (viewWidth - layout.minimumInteritemSpacing - 8) / 3, height: (viewWidth - layout.minimumLineSpacing - 8) / 3)
        
        // CollectionViewを生成.
        collectionView = UICollectionView(frame: collectionFrame, collectionViewLayout: layout)
        // Cell に使われるクラスとして CustomCell を登録
        collectionView.register(CustomCell.self, forCellWithReuseIdentifier: "MyCell")
        
        collectionView.delegate = self
        collectionView.dataSource = self
        self.view.addSubview(collectionView)
        
        // Toolbarを生成
        let toolbarHeight: CGFloat = 60
        let toolbarPaddingBottom: CGFloat = 20
        let toolbarRect: CGRect = CGRect(x: 0, y: self.view.bounds.height - toolbarHeight - toolbarPaddingBottom, width: self.view.bounds.width, height: toolbarHeight)
        toolbar = UIToolbar(frame: toolbarRect)
        toolbar?.items = self.generateToolbarButtons(isMultipleSelectionMode: self.collectionView.allowsMultipleSelection, isAnyCellselected: false)
        self.view.addSubview(toolbar!)
        
    }
    
    // Cell の総数
    func collectionView(_ collectionView: UICollectionView, numberOfItemsInSection section: Int) -> Int {
        return 36
    }
    
    // Cell に値を設定する
    func collectionView(_ collectionView: UICollectionView, cellForItemAt indexPath: IndexPath) -> UICollectionViewCell {
        let cell : CustomCell = collectionView.dequeueReusableCell(withReuseIdentifier: "MyCell", for: indexPath) as! CustomCell
        cell.contentView.backgroundColor = UIColor.yellow
        
        // 古い subview を削除
        cell.contentView.subviews.forEach { subview in
            subview.removeFromSuperview()
        }
        
        // checkmarkをつけ直す
        if CustomCell.hasCellAppearedInThePast(selectedItemAt: indexPath) {
            if CustomCell.shouldCellBeMarked(selectedItemAt: indexPath) {
                cell.mark(selectedItemAt: indexPath)
            } else {
                cell.unmark(deselectedItemAt: indexPath)
            }
        }
        
        return cell
    }
    
    // Cell がタップで選択されたときに呼ばれる
    func collectionView(_ collectionView: UICollectionView, didSelectItemAt indexPath: IndexPath) {
        guard let cell: CustomCell = collectionView.cellForItem(at: indexPath) as? CustomCell else { return }
        if self.collectionView.allowsMultipleSelection {
            cell.mark(selectedItemAt: indexPath)
        }
        let numberOfSelectedItems: Int? = collectionView.indexPathsForSelectedItems?.count
        if numberOfSelectedItems == 1 {
            let toolbarButtons: [UIBarButtonItem] = self.generateToolbarButtons(isMultipleSelectionMode: self.collectionView.allowsMultipleSelection, isAnyCellselected: true)
            self.toolbar?.setItems(toolbarButtons, animated: true)
        }
    }
    
    // Cell がタップで選択解除されたときに呼ばれる
    func collectionView(_ collectionView: UICollectionView, didDeselectItemAt indexPath: IndexPath) {
        guard let cell: CustomCell = collectionView.cellForItem(at: indexPath) as? CustomCell else { return }
        if self.collectionView.allowsMultipleSelection {
            cell.unmark(deselectedItemAt: indexPath)
        }
        let numberOfSelectedItems: Int? = collectionView.indexPathsForSelectedItems?.count
        if numberOfSelectedItems == 0 {
            let toolbarButtons: [UIBarButtonItem] = self.generateToolbarButtons(isMultipleSelectionMode: self.collectionView.allowsMultipleSelection, isAnyCellselected: false)
            self.toolbar?.setItems(toolbarButtons, animated: true)
        }
    }
    
    // Select ボタンが押されたときに呼び出される
    @objc func enableSelect(_ sender: UIBarButtonItem) -> Void {
        self.collectionView.allowsSelection = false
        self.collectionView.allowsMultipleSelection = true
        self.toolbar?.setItems(self.generateToolbarButtons(isMultipleSelectionMode: self.collectionView.allowsMultipleSelection, isAnyCellselected: false), animated: true)
    }
    
    // Cancel ボタンが押されたときに呼び出される
    @objc func disableSelect(_ sender: UIBarButtonItem) -> Void {
        let indexPaths = self.collectionView.indexPathsForSelectedItems!
        indexPaths.forEach { indexPath in
            self.collectionView.deselectItem(at: indexPath, animated: false)
        }
        
        CustomCell.clearAllCheckmarks()
        
        self.collectionView.allowsSelection = true
        self.collectionView.allowsMultipleSelection = false
        self.toolbar?.setItems(self.generateToolbarButtons(isMultipleSelectionMode: self.collectionView.allowsMultipleSelection, isAnyCellselected: false), animated: true)
    }
    
    // Toolbar のボタンを生成
    func generateToolbarButtons(isMultipleSelectionMode: Bool, isAnyCellselected: Bool) -> [UIBarButtonItem] {
        var buttons: [UIBarButtonItem] = []
        
        let addButton: UIBarButtonItem = UIBarButtonItem(barButtonSystemItem: .add, target: self, action: nil)
        let cameraButton: UIBarButtonItem = UIBarButtonItem(barButtonSystemItem: .camera, target: self, action: nil)
        let sendButton: UIBarButtonItem = UIBarButtonItem(barButtonSystemItem: .action, target: self, action: nil)
        let trashButton: UIBarButtonItem = UIBarButtonItem(barButtonSystemItem: .trash, target: self, action: nil)
        let selectButton: UIBarButtonItem = UIBarButtonItem(title: "Select", style: .plain, target: self, action: #selector(self.enableSelect(_:)))
        let cancelButton: UIBarButtonItem = UIBarButtonItem(title: "Cancel", style: .plain, target: self, action: #selector(self.disableSelect(_:)))
        let buttonGap: UIBarButtonItem = UIBarButtonItem(barButtonSystemItem: UIBarButtonSystemItem.flexibleSpace, target: nil, action: nil)
        
        let selectOrCancelButton: UIBarButtonItem
        
        if isMultipleSelectionMode {
            addButton.isEnabled = false
            cameraButton.isEnabled = false
            sendButton.isEnabled = false
            trashButton.isEnabled = isAnyCellselected ? true : false
            cancelButton.isEnabled = true
            selectOrCancelButton = cancelButton
        } else {
            trashButton.isEnabled = false
            selectOrCancelButton = selectButton
        }
        
        buttons = [addButton, buttonGap, cameraButton, buttonGap, sendButton, buttonGap, trashButton, buttonGap, selectOrCancelButton]
        return buttons
    }
    
}