Setting a focused scene value whilst the List has a selection prevents the Menu in the toolbar from opening.

MenuBug.swift

import SwiftUI

@main
struct NavigationSplitViewMenuApp: App {
    
    var body: some Scene {
        WindowGroup {
            ContentView()
        }
    }
}

struct ContentView: View {
        
    var body: some View {
        NavigationSplitView {
            Sidebar()
        } content: {
            ContentList()
        } detail: {
            Text("Detail")
        }
    }
}

struct Sidebar: View {
    
    @State private var selection = Set<Int>()

    var body: some View {
        // 1. Select an item in the list
        List(selection: $selection) {
            
            // 2. You can open me just fine
            TestMenu()

            ForEach(1...10, id: \.self) {
                Text("Item \($0)")
            }
        }
        .toolbar {
            ToolbarItem(placement: .primaryAction) {
                // 3. However you can't open me
                TestMenu()
            }
        }
        // Setting a focused scene value whilst the List has a selection
        // prevents the Menu in the toolbar from opening.
        // This is a regression from iOS 16.4.
        .focusedSceneValue(\.filterAction) {
            // do something
        }
    }
}

struct ContentList: View {
    
    var body: some View {
        List {
            ForEach(1...100, id: \.self) {
                Text("Row \($0)")
            }
        }
    }
}

struct TestMenu: View {
    
    var body: some View {
        Menu {
            Text("Catch")
            Text("Me")
            Text("While")
            Text("You")
            Text("Can")
        } label: {
            Label("New", systemImage: "plus")
        }
    }
}

struct FilterActionKey: FocusedValueKey {
    typealias Value = () -> Void
}

extension FocusedValues {
    
    var filterAction: (() -> Void)? {
        get { self[FilterActionKey.self] }
        set { self[FilterActionKey.self] = newValue }
    }
}

#Preview {
    ContentView()
}