Attack Of The Mutant (1) - S2-E2
Other mistake: In part 2, it was revealed that Libby was really the Masked Mutant all along but, in one scene in this episode, Libby is sitting next to Skipper while the Masked Mutant is standing on top of the bus.
Free Spirit - S7-E13
Other mistake: The storm has knocked out power to the facility, the emergency generator did not engage the supply power and is out of fuel, but in some parts of the building there are lights on.