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.
The Night of the Raven - S2-E3
Plot hole: Antoinette is making miniature clothes for the soon-to-be shrunken West, but when West drinks the antidote to make him normal-sized, he is wearing the same clothes which would have been shredded as he grew back to normal size.