Fear of a Krabby Patty/Shell of a Man - S4-E1
Continuity mistake: In the episode 'Shell of a Man", when SpongeBob pushes over Mr. Krabs' shell off of the chair at Mr. Krabs' desk, you can see that there are 2 eye holes, a nose hole, and a very large hole for the mouth. But when SpongeBob puts the shell on, both his nose and mouth are in the large mouth hole, and his eyes are in the eye holes. But there is no nose hole.
Fear of a Krabby Patty/Shell of a Man - S4-E1
Continuity mistake: When Mr. Krabs drags SpongeBob back into the kitchen, Squidward's facial expression changes between shots.
The Lost Mattress/Krabs vs. Plankton - S4-E2
Continuity mistake: Krabs vs. Plankton: When Krabs meets with the attorney, Bottomfeeder, both the exterior and interior door knobs on his office door appear and disappear in various shots, even consecutive shots.
Have You Seen This Snail? - S4-E3
Continuity mistake: In "Where's Gary?" the length of the paddle ball string that SpongeBob uses seems to vary in certain shots. While the length is somewhat subjective one shot that is more conclusive is when Patrick finds Spongebob lying on the floor. The string on the paddle ball is fairly short. When the two get up to get a glass of milk, the string is now a lot longer.
Have You Seen This Snail? - S4-E3
Continuity mistake: Have You Seen This Snail: After the customer asks for a refund it cuts to SpongeBob crying in the kitchen, and when Krabs walks in the door opens at the left side with no knob, but when Krabs tells SpongeBob that a problem can be solved with a little hard work, that door now opens at the right side with a door knob.
Skill Crane/Good Neighbors - S4-E4
Continuity mistake: During "Good Neighbors" SpongeBob is in Squidward's house talking to him while he is in a pink nightgown. Squidward throws SpongeBob out of his house while he is in his regular brown shirt. When he is back in his house, he is in his pink nightgown again.
Skill Crane/Good Neighbors - S4-E4
Continuity mistake: During "Good Neighbors" Squidward is sitting on his couch trying to enjoy his afternoon. SpongeBob and Patrick pop up behind him. In the next shot. Instead of Squidward sitting on his couch with Bob and Pat behind him, they are standing in the middle of the kitchen.
Skill Crane/Good Neighbors - S4-E4
Continuity mistake: In "Good Neighbors", Squidward stomps on Spongebob and Patrick's fezzes in front of his door. Then, it cuts to a shot of Squidward's house, but the fezzes are gone.
Selling Out/Funny Pants - S4-E5
Continuity mistake: In "Selling Out", at the end, all the customers leave the Krusty Krab. But when the Krusty Krab floods, the place is packed with customers.
Selling Out/Funny Pants - S4-E5
Continuity mistake: In "Selling Out", Mr. Krabs hears the footsteps of many customers approaching and the shot shows the entrance to the Krusty Krab from the inside, with no one in sight. When Mr. Krabs tells the guys that they're coming, it shows Squidward in a few shots mopping right in front of the doors, even though he wasn't seen there previously.
Selling Out/Funny Pants - S4-E5
Continuity mistake: In "Funny Pants" when Mr. Krabs tells SpongeBob to touch the money the anchor on the door is yellow. In the next shot, it is red, like it is in other episodes.
Selling Out/Funny Pants - S4-E5
Continuity mistake: In "Selling Out" when the Krabby O'Mondays is just about to flood, SpongeBob and Squidward have their Krusty Krab hats on. About ten seconds ago, they had their Krabby O' Mondays' hats on.
Enemy In-Law/Mermaidman and Barnacleboy VI: The Motion Picture - S4-E7
Continuity mistake: Patrick turned out to have put the lens cap on the camera before they started to film. But when the first scene was being filmed, there was no sign of the lens cap on the camera. There was also no sign of the lens cap on the camera when the Pearl "Boatmobile" fell off the cliff.
Patrick SmartPants/SquidBob TentaclePants - S4-E8
Continuity mistake: When SpongeBob and Squidward are combined, Squidward's arm is on the left and SpongeBob's arm is on the right, and that's how it is the whole time. Except in one shot, the shot of SpongeBob's head after Squidward says, "yellow freak." Look at the bottom and you'll see two SpongeBob arms, when the one on the left is supposed to be Squidward's.
Krusty Towers/Mrs. Puff, You're Fired - S4-E9
Continuity mistake: When the rocks fall out of Patrick's suitcase, the rocks change number and position between the 3 shots.
Krusty Towers/Mrs. Puff, You're Fired - S4-E9
Continuity mistake: When the fish is at the front desk of the Krusty Towers, there is a silver bell on the desk. When Patrick arrives, there is no bell. Then Mr. Krabs puts Squidward in his place, and the bell is back, but has moved to the opposite side of the desk.
Ghost Host/Chimps Ahoy - S4-E10
Continuity mistake: In "Ghost Host", Spongebob rips off a bit of sponge and drops it on the ground. Two shots later, his head is back to normal and the sponge on the floor is gone.
Ghost Host/Chimps Ahoy - S4-E10
Continuity mistake: In "Ghost Host", the Flying Dutchman is falling down the side of a cliff. When he lands on the ground in the next shot, the cliff is gone.
Ghost Host/Chimps Ahoy - S4-E10
Continuity mistake: In "Chimps Ahoy", a robot is lying down on a log. The robot gets up and peels the banana one of the chimps was holding. In the next shot, the log has completely disappeared.
Ghost Host/Chimps Ahoy - S4-E10
Continuity mistake: In "Chimps Ahoy", Spongebob removes a helmet he was wearing and holds it in his hands out of frame. In the next shot, the helmet is missing and not on the ground.
Answer: I believe this is the Season 6 episode "Spongicus".