This is reproducible with FX 8 and later releases, including 8u40 b06.

Please run attached TreeTableTest.java, the steps to reproduce:
1. mouse clicking on the row of "item 00 field 0" to select the root's first child.
2. click the button "remove selected". Then the row is deleted and "item 01 field 0" is highlighted with a gray bar.
3. click button "remove selected" again, the whole tree is deleted.

The button "remove selected" removes items from treeTableView.getSelectionModel().getSelectedItems(). After step 2, both root and "item 01 field 0" are selected, so the tree is deleted in step3.
Also, after step2, whatever mouse clicking on other rows, root is actually selected.

This doesn't happen with TreeView, if the first child is deleted, the root is selected and highlighted, instead of the second child.