Continuity mistake: When Sandy finds SpongeBob and Patrick after wrecking the tree dome, the distance between SpongeBob/Patrick and Sandy changes constantly between shots.
Continuity mistake: The giant Krabby Patty eats SpongeBob's shoe and sock in the kitchen. But by the time SpongeBob and Squidward run to the door and are stopped by Mr. Krabs, the shoe and sock have magically reappeared.
Other mistake: Mr. Krabs pours Sandy's growth serum on a patty. It grows, and Spongebob scrapes some off to construct individual patties from the larger one. The larger one then continues to grow, but the individual ones do not, even though they are all the same meat.
Continuity mistake: When SpongeBob and Squidward are combined, Squidward's arm is on the left and SpongeBob's arm is on the right, and that's how it is the whole time. Except in one shot, the shot of SpongeBob's head after Squidward says, "yellow freak." Look at the bottom and you'll see two SpongeBob arms, when the one on the left is supposed to be Squidward's.
Continuity mistake: In one scene where Spongebob is breathing in air, you can see the container to the right is yellow, but in the scene where he's dancing around the kitchen, it turns white.
Continuity mistake: In "One Krab's Trash," after SpongeBob discovers the drinking hat at Mr. Krabs' yard sale, the two straws are connected to a cylinder with a hole. But when Mr. Krabs says "You were born to wear this hat!" the little cylinder has vanished. Later when SpongeBob is blowing bubbles, the cylinder has reappeared.