The Secret Box / Band Geeks - S2-E14
Continuity mistake: When the band is marching through the streets, whilst Squidward is pressuring the flag twirlers to move faster, there are some fish drumming behind them. One is a blue fish wearing a yellow shirt seen standing on the left, and another is a brown fish wearing a red shirt seen standing on the right. When the flag twirlers behind to fly off the ground, those two fish have swapped places.
The Krabby Patty That Ate Bikini Bottom/Bubble Buddy Returns - S8-E15
Continuity mistake: At the beginning of bubble buddy, right after SpongeBob reads the letter from bubble buddy, Gary's swirl is blue and his spots are red.
Banned in Bikini Bottom/Stanley S. SquarePants - S5-E20
Continuity mistake: In Stanley S. Squarepants, when SpongeBob and Stanley go see Squidward when he's getting the newspaper, both Squidward and the newspaper change position in between shots.
Club SpongeBob / My Pretty Seahorse - S3-E12
Continuity mistake: In "My Pretty Seahorse", Spongebob is using a spatula with slots in it. Later, when Mystery eats it, the spatula is now completely flat.
Culture Shock / F.U.N. - S1-E10
Continuity mistake: In "F.U.N.", Mr. Krabs sets down the Krabby Patty in front of Plankton. Almost the whole plate is on the yellow part of the table, but when the camera cuts to Plankton, the plate is mostly in the red part of the table. In the next shot, the plate returns to its original position.
Squidtastic Voyage/That's No Lady - S4-E15
Continuity mistake: In "That's No Lady", Patrick runs through Spongebob's wall, leaving a Patrick-shape in his house. Patrick pushes a bit of Spongebob's house, which disappears in the next shot.
Ghoul Fools - S8-E24
Continuity mistake: When Squidward is sucked into "The Void", the bag of money that he was holding vanishes in the next shot.
Summer Job - S7-E18
Continuity mistake: Mrs. Puff didn't know that SpongeBob works at the Krusty Krab, when she already found out in 3-18 "Krusty Love." Even stranger thing, Mr. Krabs and Mrs. Puff have no idea who each other are, but they also already met in that episode.
Fools in April / Neptune's Spatula - S1-E19
Continuity mistake: In "Fools in April", Spongebob is scrubbing the floor and a customer comes up to him to ask for a couple of ice cubes. In the next shot, the water puddle on the floor gets increasingly bigger.
The Bully / Just One Bite - S2-E17
Continuity mistake: In the episode "The Bully," when Flats punches Spongebob, Spongebob states to Gary that he's made out of some spongy material, that it absorbs his blows and it doesn't hurt him at all. But in later episodes, when Spongebob gets knocked out that never happens anymore.
Procrastination / I'm With Stupid - S2-E19
Continuity mistake: Procrastination: When Gary eats all the food, he burps out his bowl. A ladder suddenly appears next to it.