Continuity mistake: When Mr. Krabs and SpongeBob are standing in front of the bomb after it lands but doesn't go off, the clock inside Mr. Krabs' office can be seen from the kitchen. The time on the clock is 5:00, but in the next shot, the time on the clock is suddenly 3:00. The bomb is then revealed to be a mechanical hand, and the time on the clock is now 5:00 again.
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.
Grandma's Kisses / Squidville - S2-E9
Deliberate mistake: Spongebob and Patrick sucks the windows off Squidward's house using leafblowers. The holes in the wall that the windows were in magically disappear.
Pre-Hibernation Week / Life of Crime - S2-E13
Continuity mistake: Sandy's bikini bottom is gone as she's bending over to paint the fence.
Help Wanted / Reef Blowers / Tea at the Treedome - S1-E2
Revealing mistake: When Spongebob uses his binoculars, his teeth turn yellow for one frame.
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.
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.
The Bully / Just One Bite - S2-E17
Continuity mistake: Just One Bite: After Squidward buries the Krabby Patty and tells SpongeBob that he hates it, when SpongeBob walks to the back door of the restaurant there's a window to the right of the door, but when Squidward makes plans to sneak a Krabby Patty that window has vanished.
The Bully / Just One Bite - S2-E17
Continuity mistake: The Bully: When Mrs. Puff enters the classroom and apologizes for being late, the door knob is at the left side of the door, but in following shots it's at the right side of the door.
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.
Continuity mistake: Rock Bottom: After SpongeBob and Patrick enter the bus, when SpongeBob asks Patrick if he has any change and for the duration of this shot, both the gear shift on the floor beside the driver and the open door of the bus have vanished, then they reappear.
Answer: I believe this is the Season 6 episode "Spongicus".