As discussed in RT-37855, there are some methods incorrectly using localToScene method.
Some of them break the MenuBar functionality when in SubScene:

public class MenuBarInSubScene extends Application {

    private static SubScene createSubScene(Paint fillPaint) {
        Group root = new Group();
        root.getChildren().add(someNodes());

        SubScene subScene = new SubScene(root, 150, 150);
        subScene.setFill(fillPaint);
        return subScene;
    }

    private static Parent someNodes() {
        final VBox vbox = new VBox();

        MenuBar bar = new MenuBar();
        final Menu foo = new Menu("Foo");
        foo.getItems().addAll(new MenuItem("X"), new MenuItem("Y"));
        bar.getMenus().addAll(foo, new Menu("Bar"));

        vbox.getChildren().add(bar);

        return vbox;
    }

    @Override
    public void start(Stage stage) {
        Group root = new Group();

        HBox hbox = new HBox();
        hbox.setTranslateY(50);
        root.getChildren().add(hbox);

        Scene scene = new Scene(root);

        SubScene plainSubScene = createSubScene(Color.GOLD);
        SubScene subSubScene = createSubScene(Color.SILVER);
        subSubScene.setHeight(75);
        subSubScene.setTranslateY(75);
        ((Group)plainSubScene.getRoot()).getChildren().add(subSubScene);
        hbox.getChildren().add(plainSubScene);

        Camera camera = new PerspectiveCamera();
        scene.setCamera(camera);
        stage.setScene(scene);
        stage.show();
    }

    public static void main(String[] args) {
        launch(args);
    }

}