Plot hole: When Jake first meets Reggie, he tells Reggie that the Great Turkey told him everything about him. Later in the movie, when Reggie goes back in time and introduces himself as the Great Turkey to a young Jake, he only tells Jake to find the "Pardoned Turkey" but never said that the pardoned turkey's name was Reggie, so there's no way the adult Jake would know Reggie's name when they first meet.
Plot hole: As shown when Robin comes under the influence of Slade's mind control device, the hypnotized people retain their abilities and higher intelligence, just with a loyalty to Slade. That being said, when Slade hypnotizes all the DC heroes, Superman and The Flash are among them in the theater. Slade orders all the heroes to chase after and destroy the Teen Titans. The Titans take off on foot with the others running after them and are able to keep their distance in a big chase sequence. Superman and The Flash never use their super speed to over take the Titans, which would have been so very easy.
Continuity mistake: When Jerry slams the door on the dollhouse after Tom attempted to catch him after his dress slips off, the blind in the top window is pulled right up but in the next shot it's now pulled down halfway.
Revealing mistake: When Alex says they should go find the penguins, he says "To home" and Marty, Melman, Gloria and Julien place their hands on top of his hand. In the next shot it shows all of them together. But due to the position of Julien and his arm length, it would have been impossible for Julien to have his hand fully placed on Alex's hand. (00:05:05)
Other mistake: At the beginning, when one bad guy is sitting on a bench with a newspaper, we can read the date October 21, 1959 at the top. But, we also read Nov 3 1970 on the same page, under the mugshot of the Boss being released from jail. (00:04:20)
Continuity mistake: When SpongeBob says he should sacrifice himself, the squidosaurs Rex has Mr. Krabs in his hands, but when SpongeBob walks to the counter, Mr. Krabs is right next to Squidward. When the camera zooms in on a group of citizens and Squidward, Mr. Krabs is gone. Then, another shot of the squidosaurs Rex, Mr. Krabs is in his hands again.
Continuity mistake: In the second scene where we first meet ranger Smith he is shuffling with some information pamphlets. When Ranger Jones yells his name he is startled and drops some of the pamphlets, but we can see that the last ones he put in were on their side. When the camera changes shots there appears to be some pamphlets sticking out. Then in the next shot they are gone. The pamphlets change locations between shots.
Audio problem: At the scene where Mikey asks the elder penguin if anyone surfs in Shiverpool, when he says,"You know you're standing on thin ice," his beak never moves.
Continuity mistake: It's shown in many scenes that the robot Gallaxar sends isn't particularly quick moving when it walks. But when it's chasing Ginormica around the city, even though Ginormica is sprinting away, it can catch her far more quickly than its speed would allow. It doesn't suddenly speed up - in the shots when the camera focuses on the robot again, you can still see it moving slowly.
Continuity mistake: During the other father's song, notice the red record player by the door and the position it's in, with the lid facing Coraline when he says, "making up a song". When the camera angle changes and he says, "she's a doll", the record player's position changes completely, with the lid now facing the wall.