When SpongeBob became The Invincibubble, he had 5 fingers instead of 4.
When Plankton got distracted by SpongeBob, he accidentally knocked over the fake bottle. But when SpongeBob and Plankton traveled back in time, the same scene was shown, but Plankton's past self didn't knock over the fake bottle.
When SpongeBob caught Plankton red-handed, he said "Uh-oh." But when SpongeBob and Plankton traveled back in time, the same scene was shown, but Plankton's past self said, "SpongeBob!", instead of "Uh-oh".
When Mr. Krabs is torturing Plankton, his headphones cover his eyestalks and not his ears.
At the sacrifice scene, Squidward first appears with his executioner mask already on, but he then puts on again in the next shot of him, even though he first appeared with the mask already worn.
The fish at the beginning referred to as "Harold" is called "Dave" in the actual show.
When Bubbles the dolphin takes SpongeBob and his friend for a ride in his mouth to get them safely to the surface, Mr. Krabs thinks they're being eaten, but SpongeBob says, "If he was eating us, he'd be chewing us up." Dolphins can rip off the flesh of animals and swallow them, but all of their teeth are sharp; therefore, they can't chew.
When the page from the book falls on top of Sandy's dome, it is much bigger then later when it hangs from her wall.
When Burger Beard's ship first hits land, the wheels do not appear to be spinning on his ship, since the hubs are completely stationary. During the chase sequence, the hubs are spinning but at irregular speeds - sometimes slowly, sometimes faster.
When King Gary's snail guards chased SpongeBob and Plankton, they were moving slowly, and SpongeBob remembered that they were snails. But at the end of the movie, Gary chased Plankton, and he got scared, even though they were moving slowly.
When SpongeBob and his friends arrived at the surface of the ocean, Squidward said that they won't be able to breathe. But in the 1st movie and the SpongeBob SquarePants TV series, they went to the surface, and they had the ability to breathe.
Even though SpongeBob gave the 1st Krabby Patty to Gary, the other customers were eating Krabby Patties at the same time.