That bug is why I always [CNTL]+[S] before processing a turn. It will also happen if one of your ninja or geisha kill a target, you've targeted that same enemy with other ninja and/or geisha, and you pick any one of them up on the same turn that the enemy was killed. When you drop it--crashola, every time.

If this happens I just [CNTL]+[L] and redo the turn.