Attack Of The Mutant (1) - S2-E2
Plot hole: Skipper spots the Masked Mutant's headquarters the first time he goes past. He then goes back the next day, and the headquarters have vanished. He then goes back a third time, and the headquarters aren't there yet again. However Skipper says "How can it be. It was right here yesterday," although it wasn't.
Answer: He repeatedly warns him against using the universal remote for bad purposes. However, Seth, blinded by remote's abilities, completely ignores and disregards Tony's warnings and uses the remote when and how he pleases, which eventually turns against him.