The Chaperone / Employee of the Month - S1-E12
Continuity mistake: When Spongebob is crying next to the employee of the month wall, (just before he says "How could I have let the quality of my work slip so much?") the order of the pictures is messed up. It goes December, February, January. Then, when we see the close-up of Squidward's face laughing, the order is correct again.
Fools in April / Neptune's Spatula - S1-E19
Continuity mistake: Eventually after Spongebob takes the door wheel handle off, it comes back.
Revealing mistake: At the beginning of Rock Bottom, when the bus pulls up in front of Patrick and SpongeBob, right before Patrick steps up onto the bus, SpongeBob's right arm is missing and it suddenly appears as he starts moving.
Krab Borg / Rock-a-Bye Bivalve - S3-E8
Revealing mistake: In the shot that shows the outside of the Krusty Krab (in Krab Borg) they reused the drawing of right before the customers ran out of the building because you can see many customers crowded at the door. This shot lasts about 2 seconds but it's not hard to spot. (00:08:05)
Spy Buddies / Boat Smarts / Good Ol' Whatshisname - S5-E4
Continuity mistake: At the beginning of Spy Buddies, when Mr. Krabs is entering the code to enter the Krusty Krab, it's night. But when Patrick yells about him wanting to be a spy and it shows the fish walking outside of the Krusty Krab, it is day.
The Algae's Always Greener / Sponge Guard On Duty - S3-E7
Continuity mistake: In "The Algae's Always Greener", after Squidward barges into Mr. Plankton's office, you can see that there are no krabby patties on Mr. Plankton's desk, but when it pans back to Mr. Plankton's desk, there are two krabby patties on his desk. (00:07:35)
Continuity mistake: When we see the "Flabby Patty" for the first time, there are 8 fish in line. When we see it the second time, there is only 5.
Jellyfishing / Plankton! - S1-E3
Other mistake: In "Jellyfishing", when SpongeBob and Patrick walk back to their houses covered in bandages, when SpongeBob says "Hey, Patrick." Patrick is mouthing what SpongeBob says.
Continuity mistake: Sometimes there is a window on the right side of Squidward's house, sometimes there's not.
20,000 Patties Under the Sea/The Battle of Bikini Bottom - S5-E17
Audio problem: In "20,000 Patties Under the Sea" When Plankton says "Ah who needs that rustbucket anyhow!" his mouth is way out of sync.
Survival of the Idiots / Dumped - S2-E8
Continuity mistake: In "Dumped", when Gary takes Patrick's cookie they are in the laundry room. When SpongeBob wants to take Gary for a walk, they instantly appear in the living room. SpongeBob also has a leash in his hand. There is no time for them to walk from the laundry room to the living room.
The Chaperone / Employee of the Month - S1-E12
Continuity mistake: In "Employee of the Month", when Spongebob is spying on Squidward, Squidward puts his alarm clock to the left of his bed. When Spongebob tries to get the clock, it is now to the right of Squidward's bed.
Pressure / The Smoking Peanut - S2-E12
Continuity mistake: When Sandy and SpongeBob are climbing the mountain at the beginning of "Pressure," when Sandy pushes the rocks down at SpongeBob, there were two big ones holding them that vanish. You could say that she pushed them down too, but remember that they were different colours than the smaller ones. (00:01:40)
Sandy's Rocket / Squeaky Boots - S1-E8
Continuity mistake: When SpongeBob is explaining why he thinks there are aliens in Sandy's Rocket, you can see a plant and rocks. We see a wide shot and it has now disappeared. (00:02:00)
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.
Something Smells / Bossy Boots - S2-E1
Continuity mistake: When Pearl gives SpongeBob the new costume for the Krusty Krab, she gives SpongeBob a mirror. In the mirror, Squidward appears and tells him not to accept the costume. If you notice, Squidward is at the LEFT of SpongeBob. Because is a mirror, in the real life he would be at the RIGHT of SpongeBob. When a shot is shown of SpongeBob and Squidward, you can see that Squidward isn't at the RIGHT of SpongeBob, he's at the LEFT.
Procrastination / I'm With Stupid - S2-E19
Continuity mistake: When Janet and Marty (Patrick's fake parents) let go of Patrick's hands in the living room, Marty is on the left. But when Janet and himself pat Patrick, his hand is to the right of Patrick.
Mermaid Man and Barnacle Boy III / Squirrel Jokes - S2-E4
Continuity mistake: In "Squirrel Jokes", right when he comes out of the curtains people put their hands up, but in a front view their hands are down.
Pizza Delivery / Home Sweet Pineapple - S1-E5
Continuity mistake: After Spongebob's house is gone, Squidward boo-hoos and goes into his house, then sounds happy. He starts throwing streamers and confetti out of his NOT-OPEN porthole. If the porthole was closed, they wouldn't fly out. Similar to some other ones in this show, and one in Fairly Odd Parents.
Sandy, SpongeBob and the Worm / Squid on Strike - S2-E18
Continuity mistake: In "Sandy, Spongebob, and the Worm," the worm is about twice the height of Sandy and Spongebob. Near the end of the episode, the Worm charges off of the cliff and when he reaches the bottom, and smashes the town, the buildings are tiny compared to him and the sea creatures are microscopic.
Answer: I believe this is the Season 6 episode "Spongicus".