Plot hole: During "the changes" people fear machinery, but the woman who pulls back her curtains to watch Nicky and the sikhs go past is wearing a watch.
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.
Episode #2.3 - S2-E3
Plot hole: Miss Summers tells her class that they have the afternoon off school due to an emergency staff meeting. Penny and Suzi leave the room with the other pupils, Miss Summers stays sitting at her desk. As the two girls are walking down the corridor out of school they stop outside the room that the meeting is in to listen. Miss Summers opens the door and tells them to go away - how did she get to the meeting when she was still sitting at her desk when Penny and Suzi left the room?
A Scooby-Doo Valentine - S3-E3
Plot hole: It's never explained how JC Chasez and the Hollywood extras impersonating the gang gained the super strength they possessed to do things like ripping car roofs open or holding up the Mystery Machine.