Patrick SmartPants/SquidBob TentaclePants - S4-E8
Continuity mistake: SquidBob TentaclePants: When the mixed-up SpongeBob and Squidward come out of Sandy's matter transporter, Squidward's arm is on the left, and SpongeBob's arm is on the right. Later on at the Krusty Krab, in the shot after Mr. Krabs tells both of them, "Alright, that's it!", we can see that both arms are SpongeBob's, when the left one is supposed to be Squidward's. (00:17:42)
Bubblestand / Ripped Pants - S1-E1
Continuity mistake: Bubblestand: When SpongeBob comes out of his house at the beginning, he leaves his front door open. Later on, when Patrick's rock opens up, the front door to SpongeBob's house is completely missing. Then, when SpongeBob hands Patrick the bubble wand, the door is back, and it is now closed. Finally, when SpongeBob and Patrick walk into the house later on, the door is open again. (00:02:30)
Hall Monitor / Jellyfish Jam - S1-E7
Continuity mistake: Hall Monitor: When SpongeBob sees the open window to the house, the window is opened to the left. When the two fish run out of the house after SpongeBob scares them, the window is opened the opposite way, then reverts back in the next shot. (00:05:19)
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.
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.