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.
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.
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.
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.
Pressure / The Smoking Peanut - S2-E12
Continuity mistake: In "Pressure" right before they all jump on land Squidward has 6 legs, but when he gets on land he has 7 legs.
Bubblestand / Ripped Pants - S1-E1
Continuity mistake: In "Bubblestand" after Squidward blows the huge bubble, he tells Spongebob and Patrick that the ability to blow bubbles is in his genes. If you look at the position of the bubblestand sign, the sign is facing the direction Squidward is talking. The sign had always been facing the street, which means that Squidward was actually talking towards the street, when Spongebob and Patrick are actually to his right.
Hall Monitor / Jellyfish Jam - S1-E7
Continuity mistake: When SpongeBob asks Squidward to play his clarinet better, he is wearing his night shirt which is purple, but in the next shot he is wearing his normal shirt which is brown.
Continuity mistake: When everybody comes to Squidward's house to persuade him to write a letter, you see that all the paper and pencils and bottles on the ground disappear.
The Great Snail Race / Mid-Life Crustacean - S3-E15
Continuity mistake: When Gary explodes or breaks down (or something like that), Snellie, Squidward's snail, rushes over to Gary. At first you see the track but the next shot (really quick) you don't see it.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In Plankton, when SpongeBob steps on Plankton, he steps on him with his left foot, except he pulls Plankton off of his right foot.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: On "One Krab's Trash", when Mr. Krabs draws a ghost on a sheet of paper, it shows before it goes into Spongebob's rooms that there's only writing on one side (i.e. the ghost) and when it goes into his room, a shopping list is on the back.
Selling Out/Funny Pants - S4-E5
Continuity mistake: In "Selling Out", at the end, all the customers leave the Krusty Krab. But when the Krusty Krab floods, the place is packed with customers.
Bubblestand / Ripped Pants - S1-E1
Continuity mistake: When Spongebob first shows Patrick the technique for bubble-blowing, there are two red corals in the background - one on his right and one on his left. Later, when he shows Squidward the technique, the red coral on the left side of the screen disappears.
Grandma's Kisses / Squidville - S2-E9
Continuity mistake: When Squidward parks his bike next to the store, he goes inside, and when he goes outside, his bike is gone.
