To reproduce open empty document in SceneBuilder, add two buttons. Try to change order of buttons by drag-n-drop in layers panel.

java.lang.NullPointerException
at com.sun.javafx.scene.control.behavior.TreeCellBehavior.doSelect(TreeCellBehavior.java:111)
at com.sun.javafx.scene.control.behavior.TreeCellBehavior.mousePressed(TreeCellBehavior.java:78)
at com.sun.javafx.scene.control.skin.SkinBase$4.handle(SkinBase.java:325)
at com.sun.javafx.scene.control.skin.SkinBase$4.handle(SkinBase.java:319)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:56)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:162)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:115)
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.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.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.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.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.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.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:2893)
at javafx.scene.Scene$MouseHandler.process(Scene.java:2687)
at javafx.scene.Scene$MouseHandler.access$1300(Scene.java:2653)
at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1279)
at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:1911)
at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:204)
at com.sun.glass.ui.View.handleMouseEvent(View.java:314)
at com.sun.glass.ui.View.notifyMouse(View.java:639)
at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at com.sun.glass.ui.win.WinApplication.access$100(WinApplication.java:29)
at com.sun.glass.ui.win.WinApplication$2$1.run(WinApplication.java:62)
at java.lang.Thread.run(Thread.java:662)