In the cartoon cut-scene, when Bart receives the Cheat Book from Frink, he is holding it in his hand. Then when he walks over to the rift portal, his hands are empty, then he has it again in the next shot.
When Bart first turns into Bartman and Homer sees him, Bart is wearing gloves. In the next shot, when Bart and Homer are walking towards the sewer, Bart is no longer wearing gloves.
At the end of Shadow Of The Colossal Donut, the Lard Lad is disconnected in the middle of Springfield. But in the hub area, Lard Lad is shown disconnected outside of Ned's house.
In the game engine in Bargain Bin, the whole Simpson family goes into the Game Engine, but when Marge says which robot is her, Lisa disappears, but reappears in the next shot.
In the first cartoon cut scene of the movie, Homer's eyes close half way just before the clip ends.
In Bargain Bin, Marge refers to the aliens as alien-octopuses, even though by that point of the game, she never seen the aliens.