Drop a MenuBar on Content Panel, select any of the 3 Menu in the Hierarchy then take Delete from the context menu: you get the stack below.

Failed to set javafx.scene.control.MenuBar.menus to [javafx.scene.control.Menu@b2929b2, javafx.scene.control.Menu@62618565]
java.lang.IndexOutOfBoundsException: Index: 2, Size: 2
    at java.util.ArrayList.RangeCheck(ArrayList.java:547)
    at java.util.ArrayList.get(ArrayList.java:322)
    at com.sun.javafx.collections.ObservableListWrapper.get(ObservableListWrapper.java:208)
    at com.sun.javafx.scene.control.skin.MenuBarSkin.rebuildUI(MenuBarSkin.java:400)
    at com.sun.javafx.scene.control.skin.MenuBarSkin.access$1100(MenuBarSkin.java:76)
    at com.sun.javafx.scene.control.skin.MenuBarSkin$6.onChanged(MenuBarSkin.java:238)
    at com.sun.javafx.collections.ListListenerHelper$SingleChange.fireValueChangedEvent(ListListenerHelper.java:134)
    at com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:48)
    at com.sun.javafx.collections.ObservableListWrapper.callObservers(ObservableListWrapper.java:97)
    at com.sun.javafx.collections.ObservableListWrapper.setAll(ObservableListWrapper.java:303)
    at com.oracle.javafx.authoring.persist.Prop$BeanProp.set(Prop.java:108)
    at com.oracle.javafx.authoring.model.transactions.SetPropertyAction.apply(SetPropertyAction.java:107)
    at com.oracle.javafx.authoring.model.transactions.Transaction.register(Transaction.java:174)
    at com.oracle.javafx.authoring.model.transactions.Transaction.removeItemFromList(Transaction.java:544)
    at com.oracle.javafx.authoring.dictionary.definition.MenuBarComponentDefinition.removeChild(MenuBarComponentDefinition.java:102)
    at com.oracle.javafx.authoring.dictionary.ComponentDictionary.delete(ComponentDictionary.java:250)
    at com.oracle.javafx.authoring.stage.Selection.delete(Selection.java:1057)
    at com.oracle.javafx.authoring.dictionary.ContextMenuController$4.handle(ContextMenuController.java:133)
    at com.oracle.javafx.authoring.dictionary.ContextMenuController$4.handle(ContextMenuController.java:119)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:69)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:217)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:170)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:37)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:53)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:28)
    at javafx.event.Event.fireEvent(Event.java:171)
    at javafx.scene.control.MenuItem.fire(MenuItem.java:425)
    at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1188)
    at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer$6.handle(ContextMenuContent.java:1139)
    at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer$6.handle(ContextMenuContent.java:1137)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:69)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:217)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:170)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:38)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:37)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:35)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:35)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:53)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:33)
    at javafx.event.Event.fireEvent(Event.java:171)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3262)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3103)
    at javafx.scene.Scene$MouseHandler.access$1900(Scene.java:3068)
    at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1506)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2222)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:227)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:523)
    at com.sun.glass.ui.View.notifyMouse(View.java:916)
SetPropertyAction(Element=Element[id=menuBar1], target=MenuBar[id=menuBar1, styleClass=menu-bar], property=javafx.scene.control.MenuBar.menus) failed
java.lang.IllegalArgumentException: Failed to set javafx.scene.control.MenuBar.menus to [javafx.scene.control.Menu@b2929b2, javafx.scene.control.Menu@62618565]
    at com.oracle.javafx.authoring.persist.Prop$BeanProp.set(Prop.java:111)
    at com.oracle.javafx.authoring.model.transactions.SetPropertyAction.apply(SetPropertyAction.java:107)
    at com.oracle.javafx.authoring.model.transactions.Transaction.register(Transaction.java:174)
    at com.oracle.javafx.authoring.model.transactions.Transaction.removeItemFromList(Transaction.java:544)
    at com.oracle.javafx.authoring.dictionary.definition.MenuBarComponentDefinition.removeChild(MenuBarComponentDefinition.java:102)
    at com.oracle.javafx.authoring.dictionary.ComponentDictionary.delete(ComponentDictionary.java:250)
    at com.oracle.javafx.authoring.stage.Selection.delete(Selection.java:1057)
    at com.oracle.javafx.authoring.dictionary.ContextMenuController$4.handle(ContextMenuController.java:133)
    at com.oracle.javafx.authoring.dictionary.ContextMenuController$4.handle(ContextMenuController.java:119)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:69)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:217)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:170)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:37)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:53)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:28)
    at javafx.event.Event.fireEvent(Event.java:171)
    at javafx.scene.control.MenuItem.fire(MenuItem.java:425)
    at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1188)
    at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer$6.handle(ContextMenuContent.java:1139)
    at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer$6.handle(ContextMenuContent.java:1137)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:69)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:217)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:170)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:38)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:37)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:35)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:35)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:53)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:33)
    at javafx.event.Event.fireEvent(Event.java:171)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3262)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3103)
    at javafx.scene.Scene$MouseHandler.access$1900(Scene.java:3068)
    at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1506)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2222)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:227)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:523)
    at com.sun.glass.ui.View.notifyMouse(View.java:916)
Caused by: java.lang.IndexOutOfBoundsException: Index: 2, Size: 2
    at java.util.ArrayList.RangeCheck(ArrayList.java:547)
    at java.util.ArrayList.get(ArrayList.java:322)
    at com.sun.javafx.collections.ObservableListWrapper.get(ObservableListWrapper.java:208)
    at com.sun.javafx.scene.control.skin.MenuBarSkin.rebuildUI(MenuBarSkin.java:400)
    at com.sun.javafx.scene.control.skin.MenuBarSkin.access$1100(MenuBarSkin.java:76)
    at com.sun.javafx.scene.control.skin.MenuBarSkin$6.onChanged(MenuBarSkin.java:238)
    at com.sun.javafx.collections.ListListenerHelper$SingleChange.fireValueChangedEvent(ListListenerHelper.java:134)
    at com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:48)
    at com.sun.javafx.collections.ObservableListWrapper.callObservers(ObservableListWrapper.java:97)
    at com.sun.javafx.collections.ObservableListWrapper.setAll(ObservableListWrapper.java:303)
    at com.oracle.javafx.authoring.persist.Prop$BeanProp.set(Prop.java:108)
    ... 41 more
Glass detected outstanding Java exception at -[GlassViewDelegate sendJavaMouseEvent:]:src/com/sun/mat/ui/GlassViewDelegate.m:507
Exception in thread "JavaFX Application Thread" com.oracle.javafx.authoring.model.transactions.Transaction$TransactionFailed: Delete failed: java.lang.IllegalArgumentException: Failed to set javafx.scene.control.MenuBar.menus to [javafx.scene.control.Menu@b2929b2, javafx.scene.control.Menu@62618565]
    at com.oracle.javafx.authoring.model.transactions.Transaction.register(Transaction.java:182)
    at com.oracle.javafx.authoring.model.transactions.Transaction.removeItemFromList(Transaction.java:544)
    at com.oracle.javafx.authoring.dictionary.definition.MenuBarComponentDefinition.removeChild(MenuBarComponentDefinition.java:102)
    at com.oracle.javafx.authoring.dictionary.ComponentDictionary.delete(ComponentDictionary.java:250)
    at com.oracle.javafx.authoring.stage.Selection.delete(Selection.java:1057)
    at com.oracle.javafx.authoring.dictionary.ContextMenuController$4.handle(ContextMenuController.java:133)
    at com.oracle.javafx.authoring.dictionary.ContextMenuController$4.handle(ContextMenuController.java:119)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:69)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:217)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:170)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:37)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:53)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:28)
    at javafx.event.Event.fireEvent(Event.java:171)
    at javafx.scene.control.MenuItem.fire(MenuItem.java:425)
    at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1188)
    at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer$6.handle(ContextMenuContent.java:1139)
    at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer$6.handle(ContextMenuContent.java:1137)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:69)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:217)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:170)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:38)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:37)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:35)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:35)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:92)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:53)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:33)
    at javafx.event.Event.fireEvent(Event.java:171)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3262)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3103)
    at javafx.scene.Scene$MouseHandler.access$1900(Scene.java:3068)
    at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1506)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2222)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:227)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:523)
    at com.sun.glass.ui.View.notifyMouse(View.java:916)
Caused by: java.lang.IllegalArgumentException: Failed to set javafx.scene.control.MenuBar.menus to [javafx.scene.control.Menu@b2929b2, javafx.scene.control.Menu@62618565]
    at com.oracle.javafx.authoring.persist.Prop$BeanProp.set(Prop.java:111)
    at com.oracle.javafx.authoring.model.transactions.SetPropertyAction.apply(SetPropertyAction.java:107)
    at com.oracle.javafx.authoring.model.transactions.Transaction.register(Transaction.java:174)
    ... 39 more
Caused by: java.lang.IndexOutOfBoundsException: Index: 2, Size: 2
    at java.util.ArrayList.RangeCheck(ArrayList.java:547)
    at java.util.ArrayList.get(ArrayList.java:322)
    at com.sun.javafx.collections.ObservableListWrapper.get(ObservableListWrapper.java:208)
    at com.sun.javafx.scene.control.skin.MenuBarSkin.rebuildUI(MenuBarSkin.java:400)
    at com.sun.javafx.scene.control.skin.MenuBarSkin.access$1100(MenuBarSkin.java:76)
    at com.sun.javafx.scene.control.skin.MenuBarSkin$6.onChanged(MenuBarSkin.java:238)
    at com.sun.javafx.collections.ListListenerHelper$SingleChange.fireValueChangedEvent(ListListenerHelper.java:134)
    at com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:48)
    at com.sun.javafx.collections.ObservableListWrapper.callObservers(ObservableListWrapper.java:97)
    at com.sun.javafx.collections.ObservableListWrapper.setAll(ObservableListWrapper.java:303)
    at com.oracle.javafx.authoring.persist.Prop$BeanProp.set(Prop.java:108)
    ... 41 more