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.
Plot hole: WARNING SPOILER AHEAD. The alien impersonating Skokes changed the ship's destination to Earth. This is impossible to have been done, as the first order the captain gave was to lock the course in and "Skokes" admits his security clearance was removed after his rescue from his prison. It also couldn't have been done by another alien spy, as no other survivors beyond the 4 (2 human and 2 aliens) were found and the only other alien spy was unconscious, so he couldn't have helped out in any way.