Doug's Shock Therapy / Doug Is Hamburger Boy - S3-E11
Plot hole: Doug recalls previous years (in a flashback, where he was next to Skeeter at the window of the Honker Burger as they looked outside) of seeing the Hamburger Boy when Mr. Dink is confessing that he *was* Hamburger Boy. However, Doug has only been living in Bluffington for one year - this was his first summer there.
Explorers on the Moon: Part 2 - S3-E12
Plot hole: In the flashback, Wolf wakes up to find out Jorgen is in his bedroom. The problem is Wolf wakes up before Jorgen even enters the bedroom.
Video Mania - S3-E6
Plot hole: The plot for this episode is that Mark reluctantly tries out video games for the first time and soon becomes addicted to them. However, the season 1 episode "All in the Family" showed him to already be an avid gamer.
Plot hole: Tim has the mike in his hand and steps repeatedly forwards to talk to Jill, the cord being long enough to allow him to do so. However once Jill leaves and he wants to go after her the mike knocks over the jar of mosquitoes. Up until then, there was no indication that the mike had been changed or moved but he never at the risk of knocking over the jar until then.