When assertions are enabled you can read the following:

Selection after close is inconsistent: did you forget to clear the selection before reparenting?

Selected element is not consistent: ComponentIndexedReference: AnchorPane[id=null]-> child #-1-> TableView[id=null, styleClass=table-view]
 scope path: /AnchorPane[id=AnchorPane]/children(@item=[SplitPane[id=null, styleClass=split-pane]])/items(@item=[AnchorPane[id=null]])/

by doing this scenario:

1. Start a layout from scratch
2. Drop a SplitPane (dropping in Hierarchy or on Content doesn't matter)
3. Drop a TableView in one of the two AnchorPane of the SplitPane
4. In Hierarchy move the TableView under top component (then out of SplitPane)

Said Daniel it is something we'd better fix: whithin Hierarchy panel's code the selection context isn't cleared as it should.