Continuity mistake: When Krabs', Squidward's and Puff's ancestors attempt to flee with the coach they pass way more buildings, seen in the background, than there actually are as shown in the overhead view of the town.
Blackened Sponge/Mermaidman vs. SpongeBob - S5-E14
Continuity mistake: In 'Blackened Sponge' a flap door suddenly appears on Spongebob's bedroom door in the background as Gary goes away to laugh.
Picture Day/Pat No Pay/Blackjack - S5-E13
Continuity mistake: In 'Picture Day' the second time Spongebob paints on the stripes on his socks they disappear in the shot where he paint rolls on his shirt/pants.
The Algae's Always Greener / Sponge Guard On Duty - S3-E7
Continuity mistake: The Algae's Always Greener: At the start, the old man is carrying a tray with just a Krabby Patty and fries, but after the old man gets the ketchup bottle Plankton zooms in on the tray, and in this closeup there's a fork and a drink with a straw beside the Krabby Patty, then they vanish.
The Algae's Always Greener / Sponge Guard On Duty - S3-E7
Continuity mistake: The Algae's Always Greener: After Plankton uses his machine and wakes up in the Krusty Krab office, he looks out through the porthole on the office door leading to the eating area, but the porthole on that office door vanishes when Plankton returns to the office with the two Krabby Patties. (00:04:25)
Banned in Bikini Bottom/Stanley S. SquarePants - S5-E20
Continuity mistake: Banned in Bikini Bottom: After the police raid the Secret Krusty Krab, Krabs and SpongeBob are both in handcuffs, but when Miss Gristlepuss trips and the Krabby Patty falls into her mouth, both pairs of handcuffs have vanished, then the handcuffs reappear again on Krabs. (00:09:45)
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 is in front of SpongeBob's body (it even moves as Patrick moves), due to an animation error in this shot. (00:09:55)
Banned in Bikini Bottom/Stanley S. SquarePants - S5-E20
Continuity mistake: Stanley S. SquarePants: When Stanley's first customer tries to place an order Stanley pulls out a camera on a tripod, and in the next shot as Stanley hugs the customer for their first picture, the kitchen door behind them does not have the usual porthole, instead it has an anchor on it just like the door to Krabs' office. (00:19:15)
Hall Monitor / Jellyfish Jam - S1-E7
Continuity mistake: Hall Monitor: After SpongeBob walks out of class the bell rings and he gets trampled, and when Mrs. Puff follows him outside the classroom door is wide open, but then the entire door suddenly vanishes.
Naughty Nautical Neighbors / Boating School - S1-E4
Continuity mistake: Boating School: When SpongeBob remembers that it's the day of the boating exam, the calendar reads "boating exam today," but then it reads "driving exam today."
Factual error: In "Wormy," when Wormy's face is viewed as a close-up in butterfly form, the wrong insect is shown. As Wormy is a butterfly, there should have been circular black eyes, long antennae and a proboscis (tongue). Instead, enormous, rainbow-colored, shimmering eyes, sharp mouthparts and horn-like antennae are seen, distinctive to that of a horsefly. Furthermore, butterflies do not make buzzing sounds, which, again, is a characteristic of flies.
Picture Day/Pat No Pay/Blackjack - S5-E13
Continuity mistake: When Patrick picks up the fridge and throws it on the barrel, there is some metal on the floor. When Mr. Krabs walks into the kitchen 2 seconds later, there is no metal on the floor.
Krusty Krushers/The Card - S6-E13
Audio problem: In "The Card", when Patrick shows SpongeBob the four special talking cards, watch carefully. You hear four punches landing on Barnacle Boy, but see only three fists come in from the right side.
Revealing mistake: After SpongeBob disguises himself as Patrick's rock and right before he sneezes his uvula clips through his bottom lip.
Jellyfish Hunters / The Fry Cook Games - S2-E16
Other mistake: When Patrick takes off Spongebob's right shoe to lick, his foot appears to be his left, not his right.
Sandy's Rocket / Squeaky Boots - S1-E8
Audio problem: When SpongeBob captures Mrs. Puff, her voice and the inflation sound are out of sync.
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.
Answer: I believe this is the Season 6 episode "Spongicus".