Continuity mistake: There's an electrical outlet on the wall below the window (aligned with the window shade's loop) in Sid's room near the Megadork poster, but when Sid throws Woody to the floor and raises the shade (before he scorches Woody's forehead with the magnifying glass), that outlet has vanished.
Continuity mistake: Early in the movie when Thomas falls overboard, John Smith ties a rope around his waist (00:02:56) and jumps in after him. Thomas is very far away from the ship (00:03:12). But when the men pull John and Thomas up, John is holding on to the rope with one hand and the end is left dangling (00:03:36). One of the men who pulled them up then coils the rope with a mere two coils (00:03:48), not nearly long enough to have reached Thomas while he was overboard. In the same scene, when we are viewing the men pulling John and Thomas up from above (00:03:38) there is no extra rope at their feet as there should have been for such a long rope.
Continuity mistake: When Max is running out of the school after successfully becoming cool. We see his friend with the orange mohawk at least twice. Once hanging from a statue, and another where he's reaching out from a school bus. These two shots are really close together so there is no way that he could have moved that quick.