Plot hole: The whole episode is based on false facts. Cody was getting an A in woodwork and Zack was failing in all his classes the previous year at school (according to their report cards in Ep "Smarter and Smarter"). So Cody knows a lot more about woodwork than Zack and should be able to make a clock, never mind a birdhouse, and Zack should not be able to make a clock.
Plot hole: The plot hinges on Kimmy finding evidence against Pastor Wayne inside of the bunker, which she ends up doing. But there's absolutely no way the police didn't thoroughly comb the bunker for evidence after discovering it. In fact, it looks like it's barely been touched in the several months that have passed. Yes, the show has a sort-of whimsical "cartoon" logic... But even in that way, it makes no sense whatsoever.
Plot hole: The Jupiter 2 crew is duplicated; however, the aliens had never seen Penny (or Judy I think). How can they be duplicated? The aliens don't have ability to know who were there, or they wouldn't have questioned Smith about the crew. Also, they do not know Smith and Will are hiding. So, they don't arm to have any special power to know beyond what they actually observe.