Welcome to the Chum Bucket / Frankendoodle - S3-E2
Character mistake: In 'Welcome to the Chum Bucket', Spongebob said he likes the grill facing the wall to the right. Plankton pushes it so that it is facing the wrong wall, the wall on the left.
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: At the end of "Welcome To The Chum Bucket", look at Spongebob's eyes. His eyebrows are more far apart than usual, also his eyeballs are uneven a bit.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Audio problem: At the end of "Born Again Krabs", SpongeBob is talking to The Flying Dutchman on the phone. SpongeBob's dialogue isn't in sync with his mouth.
Nasty Patty / The Idiot Box - S3-E4
Continuity mistake: In "The Idiot Box", Spongebob and Patrick are standing on the curb of the street and there is a building in the distance. Several shots later, they are standing in the same spot, but the building has disappeared.
As Seen on TV / Can You Spare a Dime? - S3-E5
Revealing mistake: When SpongeBob is mopping the floor, two kids walk into the background and put mustard and ketchup on their patties. Nothing is coming out of the condiment tap.
The Algae's Always Greener / Sponge Guard On Duty - S3-E7
Continuity mistake: When Plankton says, "Look at his daughter. She's as big as a whale!", the soda can on the table suddenly moves to the left.
No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: At the beginning of "Squilliam Returns," Squilliam is walking to Squidward from the left of the garbage pails. When Squidward throws his hat out, Squilliam is to the right of the garbage pails.
No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: In "No Weenies Allowed," when Spongebob gets punched by Patrick, he doesn't have a black eye. When the shot zooms to Spongebob's face, he has a black eye.
The Snowball Effect / One Krabs Trash - S3-E3
Character mistake: In the beginning of "One Krabs Trash" Spongebob only has one bill in his hand, a 5 dollar bill. When he goes to his house and comes back, he says he found 68 cents. Therefore, he has 5 dollars and 68 cents. However, he has two dollar bills and a few pennies in his hand, which cannot be made into $5.68.
Continuity mistake: When Patar heats the squished crab in the fire, it's in his left hand. But in the next shot when he eats it, it's in his right.
Wet Painters / Krusty Krab Training Video - S3-E9
Continuity mistake: When Mr. Krabs Gets Home, there is a light switch by the door, but in the next shot there is a sign instead.
Krab Borg / Rock-a-Bye Bivalve - S3-E8
Continuity mistake: Rock-a-Bye Bivalve: When Patrick gets home from the party after midnight SpongeBob is angry, and as Patrick walks out in the interior shot the front door is wide open on the inside of the home, but in the next exterior shot the front door is wide open on the outside of the pineapple.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: Mermaid Man and Barnacle Boy IV: When SpongeBob runs into the kitchen with Mermaid Man's secret utility belt, the door swings open facing away from the grill, but when Squidward demands to know what's going on in the kitchen, the door opens the opposite way.
Nasty Patty / The Idiot Box - S3-E4
Continuity mistake: Nasty Patty: After the police officer cancels his Krabby Patty order, when he tells his partner they got a call about "two ghouls burying a stiff," Krabs' office door is missing.
Nasty Patty / The Idiot Box - S3-E4
Continuity mistake: Nasty Patty: When Krabs pushes SpongeBob out of the kitchen telling him to pour on the charm for the health inspector, the door swings opens at the left side, but when SpongeBob goes back to the kitchen to order one of everything, that door opens the opposite way, then the switch happens again.
Club SpongeBob / My Pretty Seahorse - S3-E12
Continuity mistake: My Pretty Seahorse: After Krabs tells SpongeBob the restaurant is not a place for a live horse, when SpongeBob walks out with the seahorse the swinging door to the Krusty Krab's kitchen opens in the opposite direction than previous shots.
As Seen on TV / Can You Spare a Dime? - S3-E5
Continuity mistake: As Seen on TV: After SpongeBob shouts about the grand finale he tosses all the food at the hungry crowd, and as they all happily exclaim, "Krabby Patties," there is only one door to the right of Squidward's order station in this shot, though there should be two doors.
As Seen on TV / Can You Spare a Dime? - S3-E5
Continuity mistake: As Seen on TV: The front door to Mr. Krabs' office is a solid door with an anchor on the exterior side of the door, but in a few shots the office's front door has a porthole window like other doors in the restaurant.
Krab Borg / Rock-a-Bye Bivalve - S3-E8
Continuity mistake: Krab Borg: The door to Krabs' office has a porthole in many shots, but after Krabs burns his eyes he rushes out of his office into the eating area, and when he runs past Squidward and SpongeBob the office door is the normal solid door, with an anchor on the exterior side.
Chocolate With Nuts / Mermaid Man And Barnacle Boy V - S3-E11
Continuity mistake: Chocolate With Nuts: While SpongeBob and Patrick are selling chocolate, the elderly female's door opens at the left, but after Patrick claims their chocolate will make you live forever, the door is open the opposite way.
Answer: I believe this is the Season 6 episode "Spongicus".