Atlantis SquarePantis - S5-E12
Revealing mistake: Atlantis SquarePantis: After the Atlantis van crashes through the museum's ceiling, Squidward is surprised that it's the magical path to Atlantis, and while Krabs says, "Nice hot rod flames," note how only the disembodied tip of Patrick's arm clips in front of SpongeBob's body (it even moves as Patrick moves), due to an animation error in this shot. (00:09:55)
Atlantis SquarePantis - S5-E12
Continuity mistake: When SpongeBob and Patrick are in the cave, the points on the amulet change size and shape between shots.
Atlantis SquarePantis - S5-E12
Continuity mistake: When Patchy finds Encino to have shrank, he hits his peg leg against his foot. When Encino is being turned back into normal, he is wearing shoes on both feet.
Atlantis SquarePantis - S5-E12
Continuity mistake: When Plankton is placed in a jar, there is a sign that says "No Flash Photography" above him. In the next shot, this sign disappears.
Answer: I believe this is the Season 6 episode "Spongicus".