Revealing mistake: In "Not Normal" when SpongeBob says "Hmm. This video tape should help," his left arm is missing. (00:01:25)
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.
Revealing mistake: At the end of "Wormy", Patrick's eyes are missing.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: The words "Total Control" constantly appear and disappear from the controlling device in Spongebob's brain.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: In the scene where the guard pulls Mrs. Puff out of the rock yard, her hat is red, then blue, then red again throughout the cuts in the scene.
Sandy's Rocket / Squeaky Boots - S1-E8
Continuity mistake: In "Squeaky Boots", Mr. Krabs starts hearing squeaky sounds everywhere. Then he goes mad, and says he took the boots from SpongeBob. In this point, notice of the restaurant floor's color. Mr.Krabs somehow lifts the whole restaurant but we can still see some floor (where Krab is). Notice that now the color of the floor has changed.
Chocolate With Nuts / Mermaid Man And Barnacle Boy V - S3-E11
Revealing mistake: In one scene with Spongebob, Patrick, an old lady, and her almost dead mom, in one part Spongebob has no holes on his face. There is also a light-colored spot near Patrick's mouth.
Continuity mistake: When Plankton is telling Karen, "There's a whale in the laboratory," he is jumping up and down with his arms in the air, but in the next shot, his arms are suddenly down at his side.
Patrick-Man!/Gary's New Toy - S9-E2
Continuity mistake: In "Patrick-Man", in the scene after Mrs. Puff gets arrested, the guy that SpongeBob serves the krabby patty to in the Krusty Krab is not wearing a T-shirt until the guy says "Lets hope Patrick Man doesn't confiscate this one," then he is seen wearing a white T-shirt. (00:08:00)
Your Shoe's Untied / Squid's Day Off - S2-E2
Character mistake: In "Squid's Day Off", a wide shot shows Mr. Krabs exiting the hospital, except the building says" ENEREENCY" instead of "EMERGENCY."
Krusty Krushers/The Card - S6-E13
Audio problem: In "The Card", when Patrick shows SpongeBob the four special talking cards, watch carefully. You hear four punches landing on Barnacle Boy, but see only three fists come in from the right side.
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 Secret Box / Band Geeks - S2-E14
Continuity mistake: In Band Geeks during the Day Two scene, in the beginning you can see Pearl near the front, but in the distant shot that follows Pearl has moved further back. (00:04:20)
Continuity mistake: When SpongeBob accidentally reveals the location of the formula, Plankton drops the feather he is holding and lands in front of him. The feather remains on the floor, but when Pearl walks into the kitchen, the feather has suddenly vanished, and reappears in front of Plankton in the next shot.
Continuity mistake: When Mr. Krabs and SpongeBob are standing in front of the bomb after it lands but doesn't go off, the clock inside Mr. Krabs' office can be seen from the kitchen. The time on the clock is 5:00, but in the next shot, the time on the clock is suddenly 3:00. The bomb is then revealed to be a mechanical hand, and the time on the clock is now 5:00 again.
Continuity mistake: When Mr. Krabs walks into the kitchen after Plankton detonates the roof, the door falls off and there is no hinge attached to the door, but once Plankton has flown in through the hole in the roof, a hinge has suddenly appeared on the door.
Continuity mistake: After Plankton blows up the Krusty Krab roof, Mr. Krabs enters the kitchen through the door leading from his office. When he opens the door, it falls off and leans against the counter beside the door. When SpongeBob approaches Mr. Krabs, the door is suddenly lying on the floor.
Answer: I believe this is the Season 6 episode "Spongicus".