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.
Lost in Space (1965)
1 plot hole in season 3
Starring: Guy Williams, June Lockhart, Mark Goddard, Marta Kristen
Other mistake: In one of the opening scenes with Will and Dr Smith, the Robot's power pack is clearly missing.
Robot: My micromechanism thanks you, my computer tapes thank you, and I thank you.
The Great Vegetable Rebellion - S3-E23
Trivia: Due to their uncontrollable laughter during filming of the infamous "Vegetable Rebellion" episode, Guy Williams and June Lockhart were written out of the next two episodes.