Club SpongeBob / My Pretty Seahorse - S3-E12
Revealing mistake: In Club SpongeBob, when SpongeBob, Patrick and Squidward are in the forest, Squidward asks the magic conch shell if he can have something to eat. Straight after he asks "Can't you say anything else but 'No'?", it has a close-up of the shell. But Squidward's arm appears to be yellow, like SpongeBob's. This error was later corrected in 2019 when the episode was remastered for digital releases.
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.
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.
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.
The Graveyard Shift / Krusty Love - S3-E13
Continuity mistake: In "Graveyard Shift," when Squidward says to that guy they think is the hash-slinging slasher, "If that was you on the phone and you on the bus, then who was flickering the lights?" look at the "order here" sign. It says "order hear" instead of "order here," which it reads in previous shots during this episode.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Other mistake: When the citizens pop out of Sponge Bob's holes near the end of Mermaid Man and Barnacle Boy 4, if you look closely, Sandy's head is gone except her eyes and nose.
The Sponge Who Could Fly (aka The Lost Episode) - S3-E16
Trivia: The miner who gives Patchy the video tape is Stephen Hillenburg, the creator of SpongeBob SquarePants. (00:04:53)
The Snowball Effect / One Krabs Trash - S3-E3
Other mistake: One Krab's Trash: When Mr. Krabs sticks the ghost drawing in Spongebob's window with the fishing rod, the shadow of the paper is visible on Spongebob, but there is no shadow of the fishing line holding it up. (00:17:27)
Answer: I believe this is the Season 6 episode "Spongicus".