Continuity mistake: In the exterior shot of the Jupiter II landing on the planet we see through the front window that there are 2 figures in silhouette standing at the control console throughout the landing. Upon touchdown the shot changes to the interior where John Robinson and Don west are sitting behind the console and are strapped into their seats.
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.