Revealing mistake: Near the end of "Rock Bottom", when SpongeBob arrives back to Bikini Bottom, SpongeBob's pineapple is animated differently from the other buildings. It looks like it was cheaply tacked on in post production.
Enemy In-Law/Mermaidman and Barnacleboy VI: The Motion Picture - S4-E7
Other mistake: Plankton's phone doesn't have a 0 button on it.
Dying For Pie / Imitation Krabs - S2-E6
Revealing mistake: In the episode "Dying For Pie", you can see Mr. Krabs' legs disappear when Squidward says, "But you can't pay me enough to act brotherly on that guy!" Also, Squidward is standing on 2 tentacles instead of 4.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: In One Krabs Trash, Spongebob pays Mr. Krabs with what looks like two dollars, which should have been five, and when he comes back he has two dollars that doubles into four in the next shot of him leaving.
Continuity mistake: Sleepy Time: When everyone woke up SpongeBob near the end, Pearl is seen without her ponytail, but in the next shot, she has a nightcap on.
Fools in April / Neptune's Spatula - S1-E19
Continuity mistake: In "Neptune's Spatula", Patrick takes a picture of SpongeBob holding the spatula. When this happens, we can see that SpongeBob is a little worried because clouds have appeared there. However, after a while, Patrick shows the picture to Neptune, and we can see that in the picture SpongeBob is smiling and pointing with the spatula.
Something Smells / Bossy Boots - S2-E1
Continuity mistake: In Something Smells, once Spongebob finishes saying hello to all the band people, he says "Is it something I said?". You see him start to walk back but when you see a close up of him, a fire hydrant appears.
Pressure / The Smoking Peanut - S2-E12
Continuity mistake: In The Smoking Peanut, when Spongebob and Patrick are running in to see the oyster, Patrick is on the right, but in the next shot, he's on the left.
Big Pink Loser / Bubble Buddy - S2-E3
Continuity mistake: Bubble Buddy: When Spongebob brings his Bubble Buddy to the Krusty Krab, Squidward's restaurant hat is visible on his head. It is not seen when he looks into Bubble Buddy when he says, "That Bubble Buddy sure looks good."
SB-129 / Karate Choppers - S1-E14
Continuity mistake: When Spongebob throws the Krabby Patties on Squidward's head there are only 6 of them, later there's at least 8.
The Graveyard Shift / Krusty Love - S3-E13
Continuity mistake: When Squidward sees the "ghost", he gets so frightened that hair comes out of his head and his job's hat falls off. In the very next shot, the hair is gone, and the hat is there again.
Pizza Delivery / Home Sweet Pineapple - S1-E5
Audio problem: In "Pizza Delivery," when you see them being sucked towards the whirlpool (wide shot of whirlpool). Squidward says, "Let go of the pizza." several times before they actually get caught up in the whirlpool. But the time where he says the line and it automatically cuts to his face, when you see his face, it is the end of him saying the line so you hear, ".izza." You hear that, but when you see a close up of his face, his mouth is completely shut.
Continuity mistake: In "Rock Bottom" when Spongebob is on line and the egg cracks, you can see the cracked pieces on the ground and then when he does his (in pants) "Barnacles, tartar sauce" you can't see the egg pieces.
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: In the episode Welcome to the Chum Bucket, when Plankton is reading a story to SpongeBob, he is interrupted. When he looks up and sees SpongeBob asleep, Sponge doesn't have his Chum Bucket Bucket Helmet on. When Plankton decides not to hit SpongeBob with a mallet and wakes him up, Sponge has the helmet on again.
Pressure / The Smoking Peanut - S2-E12
Continuity mistake: Patrick's popcorn disappears completely after he drops it.
Something Smells / Bossy Boots - S2-E1
Continuity mistake: In Something Smells, when Spongebob is making the sundae, when he says "This sundae is gonna taste great" he has one spoon in his hand, but when he turns around, he has 2 spoons.
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.
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. At this point, notice the restaurant floor's colour. Mr. Krabs lifts the whole restaurant, but we can still see some floor (where Krabs is). Notice that now the colour of the floor has changed.
Something Smells / Bossy Boots - S2-E1
Continuity mistake: In Something Smells, when Patrick is helping Spongebob outside with the "mirror test", he pulls out the mirror and you see his face to the side of it. In the next shot he is completely behind it.
Mermaid Man and Barnacle Boy III / Squirrel Jokes - S2-E4
Continuity mistake: In Squirrel Jokes, when Spongebob comes out for his second act, there's a back shot of a crowd, and there is one guy in the front right (from the back view) who is green. There is another front shot of the crowd and the guy completely disappears.
Answer: I believe this is the Season 6 episode "Spongicus".