Yes. But, I'm not sure what, if anything, could be done to solve that.
Does it track whether such-and-such a monster is gone from the current instance? It prints it out, but setting a variable would seem dangerous, since the instance could be reset between the turn in which you set the variable and the very next turn you run. I would guess that the mechanism for determining which of skeletons/zombies it chooses to mass kill is using whichever of chainsaw chain/funhouse mirror you have the most of. If you have more mirrors than chains, it will go for skeletons - even if there are no more skeletons in this instance.
I'm not sure that CAN be fixed, since even if we noticed "there are no more skeletons", when do we reset that and decide "maybe there are more skeletons"?
I'll defer to slyz to comment on this - and, perhaps, correct what I just said.