Load an FXML file where a controller is defined, say IssueTrackingLite.fxml.
Select the current value and type say "whatever" then press ENTER.
The document is dirty, saving it and you get the new controller value ==> OK.
Now call Undo: if the controller class field is still in editing mode (editing caret is blinking in the field, or value is simply selected) the Undo will properly change the value back behind the scene but the content of the field is not modified.

The workaround is to exit edit mode (unselect the controller class value) before taking Undo command.