Continuity mistake: Throughout the whole episode of "Missing Identity", SpongeBob's shirt is backwards. This is seen with his sleeves being supposedly behind him. The sleeves are missing from the front, which is normal, but throughout the episode, pay attention to behind SpongeBob. His sleeves are supposed to be behind him, but are missing altogether.
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.
Plot hole: In the end of "Pranks A Lot" SpongeBob and Patrick glue the door shut in order to keep Mr. Krabs inside the Krusty Krab. When SpongeBob And Patrick are visible again, it turns out that a lot of customers have entered the Krusty Krab to see SpongeBob and Patrick naked. All of those people had no way to get into the Krusty Krab with the doors glued shut. It can't be that they broke down the doors, as they're still there.
Character mistake: In the beginning of "One Krabs Trash" Spongebob only has one bill in his hand, a 5 dollar bill. When he goes to his house and comes back, he says he found 68 cents. Therefore, he has 5 dollars and 68 cents. However, he has two dollar bills and a few pennies in his hand, which cannot be made into $5.68.
Continuity mistake: In "Selling Out", Mr. Krabs hears the footsteps of many customers approaching and the shot shows the entrance to the Krusty Krab from the inside, with no one in sight. When Mr. Krabs tells the guys that they're coming, it shows Squidward in a few shots mopping right in front of the doors, even though he wasn't seen there previously.
Continuity mistake: When Mr. Krabs and SpongeBob are standing in front of the bomb after it lands but doesn't go off, the clock inside Mr. Krabs' office can be seen from the kitchen. The time on the clock is 5:00, but in the next shot, the time on the clock is suddenly 3:00. The bomb is then revealed to be a mechanical hand, and the time on the clock is now 5:00 again.
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Continuity mistake: Plankton is questioning Mr. Krabs and SpongeBob for the formula whilst they are stuck inside a mechanical hand. The area where the screw is located can be seen on both sections of the hand, on the right and left hand side. In some shots the right side of the hand completely obscures the screw on the left side, and in some shots not. Also, in one shot, the screw changes colour and becomes white.
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Continuity mistake: In "Patrick's Coupon", after Patrick is released from the crane, he suspects two male fish of wanting to steal his coupons. Next, he hears two female fish talking and thinks they want his coupon too. When he goes to talk to them, the guys he was just talking to have disappeared. In two shots, the male fish reappear.
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.