Jellyfishing / Plankton! - S1-E3
Continuity mistake: In Jellyfishing, when SpongeBob and Patrick first take their nets to jellyfishing, they only take their own nets. But when they go to Squidward's house, they have another net, just for him.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In 'Plankton', when Spongebob is being controlled by Plankton and he bounces into the wall in the Chum Bucket, he is tumbling in a way so that when he is standing, he is facing away from the ingredient identifier. When the shot changes, Spongebob is now facing the identifier while standing.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: The words "Total Control" constantly appear and disappear from the controlling device in Spongebob's brain.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In "Plankton", when Plankton says tomorrow is his birthday, he is near Spongebob's thumb. When the camera zooms in on Plankton, he is instantly in the middle of Spongebob's hand.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: At the beginning of Plankton., Plankton is very small. Later in the episode, as in the rest of the show, he's bigger and not that small.
Jellyfishing / Plankton! - S1-E3
Other mistake: In "Jellyfishing", when SpongeBob and Patrick walk back to their houses covered in bandages, when SpongeBob says "Hey, Patrick." Patrick is mouthing what SpongeBob says.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: Spongebob, controlled by Plankton, wasn't aiming directly at Squidward's house, but he eventually breaks through the wall.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In "Plankton", when Plankton is controlling Spongebob, Spongebob goes to put his pants on, but Plankton has him walk through them. As they're walking towards the pants, the tie is red. As they're walking through the pants, the tie turns black. As they walk away from the pants, the tie is red again.
Jellyfishing / Plankton! - S1-E3
Character mistake: In "Plankton" when Spongebob is in Plankton's lab, he says the ingredients in a Krabby Patty. He doesn't mention the secret sauce.
Jellyfishing / Plankton! - S1-E3
Audio problem: In "Plankton" in the beginning, when Spongebob is outside with Mr. Krabs, Spongebob laughs. His laugh sounds different that how it does in the rest of the show.
Jellyfishing / Plankton! - S1-E3
Audio problem: In "Jellyfishing", in the beginning, when Squidward walks out of his house with his bike, Spongebob says "Hey, Squidward" but his mouth is saying something different.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: Plankton! When SpongeBob and Plankton are talking at night Plankton gives SpongeBob a golden spatula. When Plankton says he wants a Krabby Patty for his birthday SpongeBob drops it. Then when SpongeBob walks away, the spatula is nowhere to be seen.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In "Jellyfishing", Patrick and Spongebob slide down two ropes and burn their hands on them. The two shots after they land show them trying to cool down their hands and in the shot after that, the ropes they had just slid down on have disappeared.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In "Jellyfishing" when Squidward comes home in the bed thingy, the king jellyfish hovers above him. At first, Squidward is facing his house. But in the next shot, he is facing the road. When he replies "Ow" he is facing his house again.
Jellyfishing / Plankton! - S1-E3
Audio problem: In "Plankton!" when Mr. Krabs steps on the krabby patty, he replies with "this ain't no ghost" his mouth doesn't move at all.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In "Jellyfishing" when SpongeBob is playing Squidward's clarinet he says "Sorry, my lips are a little dry." Then he starts licking his lips. In one shot, the clarinet disappears from SpongeBob's hands. Then it reappears in the next shot.
Naughty Nautical Neighbors / Boating School - S1-E4
Continuity mistake: In 'Boating School' when Mrs. Puff blows up she has a deep voice, but in all the other episodes her voice stays the same.
Naughty Nautical Neighbors / Boating School - S1-E4
Continuity mistake: The track changes between days.
Naughty Nautical Neighbors / Boating School - S1-E4
Continuity mistake: When Patrick runs out of Spongebob's house after Spongebob cries and says he's cheating, the lower right window beside the door is gone.
Naughty Nautical Neighbors / Boating School - S1-E4
Continuity mistake: When Squidward starts making pink bubbles with messages, he goes to his backyard. Notice he never closed the back window of his house. When he starts laughing because of the messages, suddenly the window is closed. After Patrick saves Squidward, the window is still closed, but when they go to the front of his house, the window is open.
Answer: I believe this is the Season 6 episode "Spongicus".