Yes, it becomes a single wild battle with the other 2 Pokemon in wierd places. Your one has it's head through the opponents HP bar (or at least my Mew did), & theirs is just infront of your normal one (it was a Graveler). You can't select their glitched up one to attack because the game is using the single battle rules & you will attack their non-glitchy one straight away. You could also use your other one (my Mew, in this case).