Start the tool, drop any container then delete it: see attached picture. I would say it's a very recent regression.

If you try to do a resize using one of the resize handles you get these stacks:

Exception in thread "JavaFX Application Thread" java.lang.AssertionError
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.mouse.ResizeGesture.mouseDragStarted(ResizeGesture.java:111)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.mouse.AbstractMouseGesture$1.handle(AbstractMouseGesture.java:110)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.mouse.AbstractMouseGesture$1.handle(AbstractMouseGesture.java:105)
    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:54)
    at javafx.event.Event.fireEvent(Event.java:204)
    at javafx.scene.Scene$DnDGesture.fireEvent(Scene.java:2891)
    at javafx.scene.Scene$DnDGesture.process(Scene.java:2969)
    at javafx.scene.Scene$DnDGesture.access$8400(Scene.java:2867)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3705)
    at javafx.scene.Scene$MouseHandler.access$1800(Scene.java:3414)
    at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1676)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2467)
    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)
Exception in thread "JavaFX Application Thread" java.lang.NullPointerException
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.mouse.ResizeGesture.updateSceneGraphObjectSize(ResizeGesture.java:249)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.mouse.ResizeGesture.mouseDragEnded(ResizeGesture.java:146)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.mouse.AbstractMouseGesture$2.handle(AbstractMouseGesture.java:125)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.mouse.AbstractMouseGesture$2.handle(AbstractMouseGesture.java:120)
    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:54)
    at javafx.event.Event.fireEvent(Event.java:204)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3689)
    at javafx.scene.Scene$MouseHandler.access$1800(Scene.java:3414)
    at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1676)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2467)
    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)