Plot holes: Spongebob points out that he has been awarded Employee of the Month award 374 times in a row. That would mean that he would have worked at the Krusty Krab for 31 years and yet he's referred to as a kid.
Continuity: When Neptune originally enters the Krusty Krab 2, if you look out the window the original Krusty Krab isn't there.
Continuity: Karen did not have the button that Plankton pushes in The Chum Bucket in front of Squidward in the beginning of the movie.
Miscellaneous: In the beginning of the movie during Spongebob's dream Mr. Krabs says,"When the costumer took a bite... No Cheese!" But when Spongebob lifts the bun you can clearly see that there are not any teeth or bite marks.
Continuity: The length of Spongebob and Patrick's "Facial Hair" changes frequently. You can clearly see during the "Now that we're men" scene that the "Facial Hair" is so long that it stretches off of there mouths but when you see their backs when they are jumping rocks you cant see the "Facial Hair" you can also see it during other shots.
Continuity: At the end when Plankton says,"No because I'm an evil genius, and you're just a kid, a stupid kid." In the Krusty Krab, during the close-up shots of Plankton you can see there is only 1 nail attached to the floor next to the Register, but when Plankton walks next to Karen and Neptune and you see Spongebob do his speech you can clearly see that there are now 3 nails attached to the floor.
Continuity: When Goofy Goober is singing the theme song, he starts the song with his lollipop in his hand, but when the finger pointing to the kids pops out of his chest, the lollipop disappears and in the next scene the lollipop is in his hands again as he sweeps it around.
Continuity: In the courtroom scene with King Neptune, Mindy's gold wrist band keep disappearing and reappearing.
Continuity: In the beginning, when Spongebob walks out of the wall of foam after he cleans himself, he is wearing underwear. Yet when he puts on his pants and looks in the mirror, and the back part of the pants fall down, we see he isn't wearing any.
Continuity: Towards the end of the movie, the bucket head people walk through the windows of the Krusty Krab, breaking them. In the very next shot you can see windows fixed.
Revealing mistakes: When Patrick and SpongeBob are trapped in the fishbowl in Shell City, there is one shot where the gravel in the bottom is reflected on the side, but Patrick and SpongeBob are not in the reflection.
Factual errors: In the scene where they are in the shell city, smoke from the outlet causes the water sprinklers to spray the store. In real life the water sprinklers in the ceiling detect heat, not smoke. Furthermore, only the sprinklers that got hot enough to fuse their elements will permit water flow, not the entire sprinkler system.
Continuity: Before the chase scene between Spongebob, Patrick, and the monster who has a tongue dressed as an old lady, the tongue's old lady costume falls off. Then, during the chase, it is back on again.
Revealing mistakes: King Neptune puts a lock on the door to make sure Mindy does not get back in but when the bucket heads break through there is no lock on the door.
Errors made by characters (possibly deliberate errors by the filmmakers): Plankton's size alternates at different scenes in the movie. After Spongebob steps on him, he is about as tall as the top of Spongbob's shoe. At the end when everyone is talking to Plankton, he is as tall as one of the stripes on Spongebob's socks.
Continuity: When Mr. Krabs and King Neptune hear Plankton's fake message, at the end we hear the click of the phone hanging up; yet when King Neptune bellows with rage a few minutes later Plankton is still on the phone as he is able to hear it.
Revealing mistakes: The "Cyclops" Diving suit that captures Spongebob and Patrick has no air supply.