To reproduce:
1. Add an AnchorPane then add a GridPane(2x3).
2. Delete the columns of GridPane one by one, until the last column is deleted.
3. On Hierarchy Panel, the GridPane still there with node id GridPane(1x3). But Content Panel, the it's already out of the range.
4. Now add a Button to the GridPane on Hierarchy Panel.

IndexOutOfBoundsException is reported, please refer to the attached error-log.txt.