Factual error: In "Wormy," when Wormy's face is viewed as a close-up in butterfly form, the wrong insect is shown. As Wormy is a butterfly, there should have been circular black eyes, long antennae and a proboscis (tongue). Instead, enormous, rainbow-colored, shimmering eyes, sharp mouthparts and horn-like antennae are seen, distinctive to that of a horsefly. Furthermore, butterflies do not make buzzing sounds, which, again, is a characteristic of flies.
Revealing mistake: When we see Billy get told about the stupid squirrel, he has a sleeve going through his arm. The moment he starts talking, the sleeve disappears and his arm extends over his shirt. Around the end of the shot when he's being pulled away, the sleeve returns.
Plot hole: In "Pranks A Lot", Patrick and SpongeBob scare Sandy. When Sandy runs, gets into her rocket and flies away. When she moved bubbles appeared meaning there's water in her tree house. There's no water in there in other episodes because she's a land animal and breathes air.
Plot hole: When the invisible Spongebob and Patrick scare Sandy, they are using a sheet to appear as "ghosts". However, the form of the sheet reveals that they don't have their helmet bowls on. How could they survive in the treedome that time? They sounded fine, not dehydrated.
Character mistake: In "I Heart Dancing", the lady at the Krusty Krab tells Spongebob the dancing audition is the next day. Later, Spongebob is practicing at Squidward's house for a whole night, and the next morning Squidward says they have one more day to practice, even though the audition should have been that day.
Plot hole: As Spongebob is trying to let the Jellyfish out of their enclosure after discovering what Mr Krabs is doing to them, Krabs says, "That door will only open if I say...open." Then he suddenly realises what he's said and the door opens. How come the door didn't open when in his sentence he first said open? The door didn't activate itself until he said open the second time.
Revealing mistake: In Club SpongeBob, when SpongeBob, Patrick and Squidward are in the forest, Squidward asks the magic conch shell if he can have something to eat. Straight after he asks "Can't you say anything else but 'No'?", it has a close-up of the shell. But Squidward's arm appears to be yellow, like SpongeBob's. This error was later corrected in 2019 when the episode was remastered for digital releases.
Plot hole: In "Mermaid man and Barnacle Boy", Plankton is shown as taller than the town at the end of the episode. However, when Spongebob is shrinking the people of Bikini Bottom, their sizes in the pickle jar seem to be equal with Plankton's actual height. In reality, Plankton should have been around the same size as the rest of Bikini Bottom's residence after the shrinking, not 5 times taller.
Continuity mistake: In "Where's Gary?" the length of the paddle ball string that SpongeBob uses seems to vary in certain shots. While the length is somewhat subjective one shot that is more conclusive is when Patrick finds Spongebob lying on the floor. The string on the paddle ball is fairly short. When the two get up to get a glass of milk, the string is now a lot longer.