With SB 2.0 b12 :
- if you load attached inluded1.fxml
- then select FXML included element
- then invoke Edit -> Trim Document to Selection
you will get :

Exception in thread "JavaFX Application Thread" java.lang.AssertionError
at com.oracle.javafx.scenebuilder.kit.editor.job.ModifyFxControllerJob.<init>(ModifyFxControllerJob.java:52)
at com.oracle.javafx.scenebuilder.app.info.InfoPanelController.updateController(InfoPanelController.java:229)
at com.oracle.javafx.scenebuilder.app.info.InfoPanelController.sceneGraphRevisionDidChange(InfoPanelController.java:118)
at com.oracle.javafx.scenebuilder.kit.editor.panel.util.AbstractPanelController$2.changed(AbstractPanelController.java:189)
at com.oracle.javafx.scenebuilder.kit.editor.panel.util.AbstractPanelController$2.changed(AbstractPanelController.java:186)
at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:347)
at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
at javafx.beans.property.IntegerPropertyBase.fireValueChangedEvent(IntegerPropertyBase.java:106)
at javafx.beans.property.IntegerPropertyBase.markInvalid(IntegerPropertyBase.java:113)
at javafx.beans.property.IntegerPropertyBase.set(IntegerPropertyBase.java:146)
at com.oracle.javafx.scenebuilder.kit.fxom.FXOMDocument.refreshSceneGraph(FXOMDocument.java:274)
at com.oracle.javafx.scenebuilder.kit.fxom.FXOMDocument.endUpdate(FXOMDocument.java:254)
at com.oracle.javafx.scenebuilder.kit.editor.job.BatchJob.execute(BatchJob.java:120)
at com.oracle.javafx.scenebuilder.kit.editor.job.TrimSelectionJob.execute(TrimSelectionJob.java:123)
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.EditorController.performEditAction(EditorController.java:948)
at com.oracle.javafx.scenebuilder.app.menubar.MenuBarController$EditActionController.perform(MenuBarController.java:1468)
at com.oracle.javafx.scenebuilder.app.menubar.MenuBarController.handleOnActionMenu(MenuBarController.java:1080)
at com.oracle.javafx.scenebuilder.app.menubar.MenuBarController.access$800(MenuBarController.java:88)
at com.oracle.javafx.scenebuilder.app.menubar.MenuBarController$20.handle(MenuBarController.java:1073)
at com.oracle.javafx.scenebuilder.app.menubar.MenuBarController$20.handle(MenuBarController.java:1069)
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.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:49)
at javafx.event.Event.fireEvent(Event.java:204)
at javafx.scene.control.MenuItem.fire(MenuItem.java:462)
at com.sun.javafx.scene.control.GlobalMenuAdapter$5.handle(GlobalMenuAdapter.java:158)
at com.sun.javafx.scene.control.GlobalMenuAdapter$5.handle(GlobalMenuAdapter.java:156)
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.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 javafx.scene.control.MenuItem.fire(MenuItem.java:462)
at com.sun.javafx.tk.quantum.GlassSystemMenu$6.action(GlassSystemMenu.java:234)