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.
Continuity mistake: When SpongeBob accidentally reveals the location of the formula, Plankton drops the feather he is holding and lands in front of him. The feather remains on the floor, but when Pearl walks into the kitchen, the feather has suddenly vanished, and reappears in front of Plankton in the next shot.
Continuity mistake: When Plankton is telling Karen, "There's a whale in the laboratory," he is jumping up and down with his arms in the air, but in the next shot, his arms are suddenly down at his side.
The Inmates of Summer/To Save a Squirrel - S5-E15
Continuity mistake: In "The Inmates of Summer", the campers that board the boat while Spongebob and Patrick are crying together throw confetti that lands on top of their puddle of tears. When the inmates start boarding in a few shots, a wide shot shows the confetti has disappeared and the next shot, which is closer, also shows the confetti to have vanished.
The Inmates of Summer/To Save a Squirrel - S5-E15
Continuity mistake: In "To Save a Squirrel", Sandy has oil stains all over her suit from working on her vehicle. After she is tackled by Spongebob and Patrick when they were chased by a grasshopper in two shots, the stains disappear.
The Inmates of Summer/To Save a Squirrel - S5-E15
Continuity mistake: In "To Save a Squirrel", Spongebob is slowly losing his mind in the mud replica of the Krusty Krab and he begins to make a fake Krabby Patty out of mud. He says he needs buns and suddenly two pieces of rock appear next to him that weren't there before.
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.
The Secret Box / Band Geeks - S2-E14
Continuity mistake: In Band Geeks during the Day Two scene, in the beginning you can see Pearl near the front, but in the distant shot that follows Pearl has moved further back. (00:04:20)
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".