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 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)
The Snowball Effect / One Krabs Trash - S3-E3
Other mistake: In 'The Snowball Effect' when Squidward attempts to make Patrick and Spongebob resume their snowball fight he throws a snowball at them which they avoid, and it puts out Squidward's fire inside. Squidward had his back towards his house and threw the snowball in the opposite direction.
No Weenies Allowed / Squilliam Returns - S3-E6
Other mistake: Squilliam Returns: After Squilliam tells Squidward that he is a cashier just like him, Mr. Krabs is shown playing his small violin, but his eyes are coloured white instead of their usual pale green colour. (00:23:07)
SpongeBob's House Party (aka Party Pooper Pants) - S3-E10
Other mistake: When Patchy pops Minnie Mermaid's pool, water comes out from a different place.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Other mistake: Born Again Krabs: When the Flying Dutchman gives Mr. Krabs the choice of either taking SpongeBob or all the money in his pocket, the Flying Dutchman says he has 62 cents, and Mr. Krabs says he will take the money. In the next shot of SpongeBob, his right leg is missing. (00:10:35)
Other mistake: In the credits, Tom Kenny, Bill Fagerbakke, and Rodger Bumpass are credited for playing SpongeBob, Patrick, and Squidward. However, Patrick and Squidward's names should be "Patar" and "Squog," and "SpongeGar" should be shown along with SpongeBob's name (SpongeBob makes a small appearance near the start of the episode). (00:22:32)
Other mistake: When the credits say that the live-action island footage is by Bad Clams Productions, Inc, there is a missing space between the words "footage" and "by." (00:22:55)
Krabby Land / The Camping Episode - S3-E19
Other mistake: In "Krabby Land", Mr. Krabs as "Krabby The Clown" finishes his short speech and goes into his office. When he slams the door, bubbles float up and those bubbles stay motionless in the air for a few frames.
SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Other mistake: Pranks a Lot: When everyone is cheering on SpongeBob and Patrick at the end, Sandy whistles by putting her hand through her helmet. Impossible. (00:23:30)
Answer: I believe this is the Season 6 episode "Spongicus".