Continuity mistake: At the beginning of Spy Buddies, when Mr. Krabs is entering the code to enter the Krusty Krab, it's night. But when Patrick yells about him wanting to be a spy and it shows the fish walking outside of the Krusty Krab, it is day.
Audio problem: In "Slimy Dancing" in the scene where Squidward and Spongebob perform their act, we first see Squidward making Spongebob spin around. There's a shot where it shows Squidward inside Spongebob. The curtain in the background in the shot remains still, even though you can hear spinning.
Factual error: In 'A Flea in Her Dome' Sandy opened up the door for water to fill her dome. The water even replaced the air on the inside which was above the door, which isn't possible because the air would have to go down through the door to escape the dome.
Continuity mistake: In "Good Ol' Whatshisname", Squidward is seen marking his calendar which has five weeks on it, and each row has a set of numbers. In the next shot, when it shows the rest of Squidward's jail cell, the bottom two rows of the calendar are completely blank.
Continuity mistake: In "Good Ol' Whatshisname", Squidward uses a pencil to mark his calendar and sets it down on his bench when Mr. Krabs and Spongebob come to visit them. He goes up to the bars, and in a few shots, when it cuts to him, you can see the bench he was just on and the pencil has disappeared.
Continuity mistake: In "The Krusty Plate", Spongebob finds that one plate has a brown smudge on it. After an attempt to clean the plate, he lifts it up and the smudge is now a light shade of green.