I think others have reported no buttons against dark trooper before. Seems to be when he gets counter attacked, as I think many of the other reports are to do with CLS teams against troopers.
It could be that the counter attack is happening in dark trooper's turn, you kill the instance of trooper that was taking its turn. He gets replaced with the new fresh one, but the game is trying to go back to the dead one's turn to resolve the end of turn stuff, but he's not there.
Try a different team, or don't link straight away, so you don't get retribution. Use mass assist to take him down instead. Focus dark down before getting retribution.