When moving around previously wrapped content. The attached file seems to still contain the bad structure,
GridPane located in AnchorPane/SplitPane/Tab Pane/Configuration display a yellow triangle in the Hierarchy when re-opening it.
 

java.lang.IndexOutOfBoundsException: Index: 4, Size: 4
        at java.util.ArrayList.rangeCheck(ArrayList.java:638)
        at java.util.ArrayList.get(ArrayList.java:414)
        at com.oracle.javafx.scenebuilder.kit.editor.job.gridpane.v2.InsertColumnConstraintsJob.redo(InsertColumnConstraintsJob.java:107)
        at com.oracle.javafx.scenebuilder.kit.editor.job.gridpane.v2.InsertColumnConstraintsJob.execute(InsertColumnConstraintsJob.java:89)
        at com.oracle.javafx.scenebuilder.kit.editor.job.v2.CompositeJob.execute(CompositeJob.java:98)
        at com.oracle.javafx.scenebuilder.kit.editor.job.BatchJob.execute(BatchJob.java:117)
        at com.oracle.javafx.scenebuilder.kit.editor.job.BatchJob.execute(BatchJob.java:117)
        at com.oracle.javafx.scenebuilder.kit.editor.JobManager.executeJob(JobManager.java:181)
        at com.oracle.javafx.scenebuilder.kit.editor.JobManager.push(JobManager.java:70)
        at com.oracle.javafx.scenebuilder.kit.editor.drag.DragController.end(DragController.java:125)
        at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.dragDoneOnGlassLayer(DragGesture.java:409)
        at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.access$500(DragGesture.java:75)
        at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture$5.handle(DragGesture.java:155)
        at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture$5.handle(DragGesture.java:151)
        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.processDropEnd(Scene.java:3062)
        at javafx.scene.Scene$DnDGesture.access$6800(Scene.java:2896)
        at javafx.scene.Scene$DragSourceListener.dragDropEnd(Scene.java:3306)
        at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler$6.run(GlassSceneDnDEventHandler.java:150)
        at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler$6.run(GlassSceneDnDEventHandler.java:145)
        at java.security.AccessController.doPrivileged(Native Method)
        at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.handleDragEnd(GlassSceneDnDEventHandler.java:145)
        at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleDragEnd(GlassViewEventHandler.java:615)
        at com.sun.glass.ui.View.handleDragEnd(View.java:652)
        at com.sun.glass.ui.View.notifyDragEnd(View.java:966)
        at com.sun.glass.ui.mac.MacPasteboard._putItemsFromArray(Native Method)
        at com.sun.glass.ui.mac.MacPasteboard.putItemsFromArray(MacPasteboard.java:143)
        at com.sun.glass.ui.mac.MacPasteboard.putItems(MacPasteboard.java:165)
        at com.sun.glass.ui.mac.MacSystemClipboard.pushToSystem(MacSystemClipboard.java:223)
        at com.sun.glass.ui.SystemClipboard.flush(SystemClipboard.java:51)
        at com.sun.glass.ui.ClipboardAssistance.flush(ClipboardAssistance.java:59)
        at com.sun.javafx.tk.quantum.QuantumClipboard.flush(QuantumClipboard.java:274)
        at com.sun.javafx.tk.quantum.QuantumToolkit.startDrag(QuantumToolkit.java:1150)
        at javafx.scene.Scene$DnDGesture.dragDetectedProcessed(Scene.java:2940)
        at javafx.scene.Scene$DnDGesture.process(Scene.java:3009)
        at javafx.scene.Scene$DnDGesture.access$8400(Scene.java:2896)
        at javafx.scene.Scene$MouseHandler.process(Scene.java:3762)
        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)