To reproduce:
-add grid pane to the content panel
-add button to cell (0,0) (first col and first row)
-select the button and increase row span 2 times(using modify-grid pane - increase row span)
-select and remove last 2 rows using button "-" at layout panel
-take a look at selected grid pane -- at the bottom of grid there is extra row with number "2"(to see it's number just select the row)