Load some fxml file, then modify it.
Now quit the tool using accelerators (cmd + Q).
Save or not the dirty file, you will get the following assertion :

Exception in thread "JavaFX Application Thread" java.lang.AssertionError
at com.oracle.javafx.scenebuilder.kit.editor.panel.content.mode.EditModeController.mouseExitedGlassLayer(EditModeController.java:616)
at com.oracle.javafx.scenebuilder.kit.editor.panel.content.mode.EditModeController.access$100(EditModeController.java:93)
at com.oracle.javafx.scenebuilder.kit.editor.panel.content.mode.EditModeController$2.handle(EditModeController.java:502)
at com.oracle.javafx.scenebuilder.kit.editor.panel.content.mode.EditModeController$2.handle(EditModeController.java:499)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
at javafx.event.Event.fireEvent(Event.java:204)
at com.sun.javafx.event.EventQueue.fire(EventQueue.java:48)
at javafx.scene.Scene$MouseHandler.handleEnterExit(Scene.java:3662)
at javafx.scene.Scene$MouseHandler.process(Scene.java:3728)
at javafx.scene.Scene$MouseHandler.access$1800(Scene.java:3471)
at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1695)
at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2486)
at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:314)
at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:243)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:345)
at com.sun.glass.ui.View.handleMouseEvent(View.java:526)
at com.sun.glass.ui.View.notifyMouse(View.java:898)
at com.sun.glass.ui.mac.MacWindow._setView(Native Method)
at com.sun.glass.ui.Window.setView(Window.java:383)
at com.sun.javafx.tk.quantum.WindowStage.setScene(WindowStage.java:257)
at javafx.stage.Window$9.invalidated(Window.java:782)
at javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:109)
at javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:143)
at javafx.stage.Window.setShowing(Window.java:826)
at javafx.stage.Window.hide(Window.java:851)
at javafx.stage.Stage.close(Stage.java:1136)
at com.oracle.javafx.scenebuilder.kit.editor.panel.util.AbstractWindowController.closeWindow(AbstractWindowController.java:157)
at com.oracle.javafx.scenebuilder.app.SceneBuilderApp.closeWindow(SceneBuilderApp.java:409)
at com.oracle.javafx.scenebuilder.app.SceneBuilderApp.documentWindowRequestClose(SceneBuilderApp.java:195)
at com.oracle.javafx.scenebuilder.app.DocumentWindowController.performCloseAction(DocumentWindowController.java:1804)
at com.oracle.javafx.scenebuilder.app.DocumentWindowController.onCloseRequest(DocumentWindowController.java:1047)
at com.oracle.javafx.scenebuilder.kit.editor.panel.util.AbstractWindowController$1.handle(AbstractWindowController.java:62)
at com.oracle.javafx.scenebuilder.kit.editor.panel.util.AbstractWindowController$1.handle(AbstractWindowController.java:59)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
at javafx.event.Event.fireEvent(Event.java:204)
at com.sun.javafx.stage.WindowPeerListener.closing(WindowPeerListener.java:80)
at com.sun.javafx.tk.quantum.GlassStage$2.run(GlassStage.java:201)
at com.sun.javafx.tk.quantum.GlassStage$2.run(GlassStage.java:198)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.tk.quantum.GlassStage.requestClosingAllWindows(GlassStage.java:198)
at com.sun.javafx.tk.quantum.QuantumToolkit$15.handleQuitAction(QuantumToolkit.java:345)
at com.oracle.javafx.scenebuilder.app.AppPlatform$MacEventHandler.handleQuitAction(AppPlatform.java:284)
at com.sun.glass.ui.mac.MacApplication$7.action(MacApplication.java:169)

When using the menu item, there is no assertion error.