I had that happen earlier today with heroes. When I looked closely at the little circles with the hero picture the two heroes I had that were the same type were stacked together - there was a little 2 on the picture.
When I clicked only that one unit and moved him out of the town it moved both the heroes.
Was a moment of panic trying to figure out what the heck happened.
Not sure if this is what you are experiencing but it sounds the same!
