
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: Frankendoodle: When DoodleBob first starts beating up Squidward, the door to Squidward's house is open, but two shots later, the door has completely vanished. (00:16:32)

Sandy, SpongeBob and the Worm / Squid on Strike - S2-E18
Continuity mistake: Sandy, SpongeBob, and the Worm: When SpongeBob makes a necklace out of the paper clip and string, he holds up the paper clip that he made into an "S" shape as he wears the necklace. In the next shot, the paper clip is facing the opposite way, then reverts back in the following shot. (00:22:20)
Krabby Land / The Camping Episode - S3-E19
Continuity mistake: Krabby Land: When Mr. Krabs sticks his head out of his office near the start, the door to his office is missing, but then it appears a moment later. (00:01:42)

Krabby Land / The Camping Episode - S3-E19
Continuity mistake: Krabby Land: After Mr. Krabs speaks to the children as Krabby the Clown, he goes inside his office. Then, when SpongeBob starts talking to Mr. Krabs, the door to Mr. Krabs' office has vanished; then it reappears a moment later. (00:10:18)

Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: Frankendoodle: When SpongeBob pranks Squidward by pulling the dollar away from him, Squidward's monocle falls on the ground, but when the mustache flies away, the monocle has vanished. A chain on the monocle also appears in one shot, then disappears. (00:15:47)
You Wish ('Shanghaied') / Gary Takes A Bath - S2-E11
Continuity mistake: Gary Take a Bath: The huge mud puddle around the tree was never there when SpongeBob first heard Gary's meows coming from the tree. In addition, when SpongeBob first looks down at Gary from the tree, the mud puddle is about the size of Gary, but in the next shot, it becomes tremendously bigger. (00:21:34 - 00:22:10)

Survival of the Idiots / Dumped - S2-E8
Continuity mistake: Dumped: When SpongeBob gives Larry the Snail dinner, Larry is sitting on two books placed on a chair. Then, as Larry smells the food, the bottom book is now facing a different direction. (00:19:54)
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In Plankton! When Plankton pulls out a radio player to play his evil music on SpongeBobs pillow, it has disappeared when Spongebob wakes up. SpongeBob didn't move on it.
Procrastination / I'm With Stupid - S2-E19
Continuity mistake: In "Procrastination" when Spongebob is moving back and forth on his chair while writing his essay there is no pencil on the desk, but when he goes back to work on the essay there is.
Suggested correction: The pencil is sitting to the right of the paper the entire time. It's hard to notice at first, but it's there.
SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Continuity mistake: When The Strangler and Spongebob arrive at the pineapple, look at the door: there is no doormat below it, but a couple minutes later Spongebob pulls a key out from under the doormat that was not there before.
Continuity mistake: When all of Spongebob's friends are formed around him, there's one scene where Pearl's hat disappears and then reappears, so for a few seconds she's completely bald. Her hair isn't even there.

The Secret Box / Band Geeks - S2-E14
Continuity mistake: When SpongeBob is sneaking to Patrick's house, Squidwards house is missing.
Something Smells / Bossy Boots - S2-E1
Continuity mistake: In "Something Smells," when SpongeBob is playing the organ at night, he turns around and his glasses are on. In 2 of the 3 shots, the glasses disappear.
Have You Seen This Snail? - S4-E3
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.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In Jellyfishing, when Patrick puts the net in Squidward's hand, at first it is in his left hand, but when he gets the jellyfish on the king jellyfish, it is on his right hand.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: Spongebob crashes through Squidward's house, and his bedroom is on the bottom floor. But in "Shanghied" after Squidward exits the fly of doom, you can see his bedroom is on the top floor, as it is in other episodes.

SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Continuity mistake: In "Pranks-A-Lot" when Sandy flies out of her dome in an escape pod to Texas, she leaves a big hole on top of her dome. In the next shot, it's gone. Very noticeable mistake.
Continuity mistake: Plankton's Army (aka Plankton's Last Stand) / Missing Identity: When the screen splits into 4, the last 2 events are not in chronological order. That is, they are not in the same order as they always have been.
Continuity mistake: The Krusty Krab kitchen sometimes has deep fryers, and sometimes it doesn't. When it does, the fryers change locations in the room between episodes.
Continuity mistake: In the episode "Missing Identity", when Spongebob is talking to Patrick about saying "hi" to him the first time, Squidward's house is gone.