When Hanson puts his hand in the pie, we see Shorty, Theo and Alex get up form the table and leave. But when the angle changes two seconds later. Alex is still sitting at the table, then throws her hand cloth and leaves the table.
When Cindy, Brenda and Buddy reunite after being chased by the skeleton, Hugh Kane gives Buddy a wedgie and Buddy has white underwear. But when Cindy and Buddy are trapped in the science room, and when Buddy unzips his pants his underwear is green.
When Puss and Cindy are fighting the, cat claws Cindy on the cheek and causes her lip to bleed. When Cindy is having breakfast with the professor the next morning, the scratches from the cat are on her chest and there is no wound on her lip.
When Professor Oldman is talking to the group in the school auditorium, there is a briefcase on the stage behind him to the right that is open. Though you never see anyone touch the briefcase, the briefcase is closed when he is finishing the meeting.
When Dwight is handing out the thermal goggles he leaves one pair on the shelf. One cut later (with the camera still on him) the last pair of goggles end up on his lap. The next shot, there are no thermal goggles left on the shelf.
When Ray goes to grab Cindy off the platform near the end of the movie, you can see the staircase behind Ray as he begins to run towards Cindy. There's only one staircase in the movie and there should have been Cindy and Hugh Kane (the ghost) in front of the staircase, but they are nowhere to be seen while Ray is running towards them. They appear when Ray grabs Cindy off the platform.
An odd bulge in the sleeve makes the presence of the robotic device that controls Hanson's mutated hand obvious. As well, the sleeve of that arm is clearly empty, indicating that the actor's real arm is tucked under his clothes, perhaps even controlling the robotic hand.
When Cindy is at the hotdog stand with Hanson we see the remote/battery pack for her mic on her back. When she turns, we see the mic wire running up to her shirt (this has been fixed in the DVD release).
When Dwight walks into the lab after falling off the ledge, Buddy and Ray help him off the floor. Between close-ups, Rays shirt turns from yellow to orange then yellow then orange again and then back to yellow.
When Cindy begins fist fighting with Hanson (before she forms the tornado), for a split second you can see that the movie actually cuts to a shot of Theo fighting with Hanson, and not Cindy. This is noticeable as Cindy is wearing a white top, while Theo is wearing black.