Grandma's Kisses / Squidville - S2-E9
Continuity mistake: When Spongebob stops crying, his grandma pulls a plug out of the floor to drain the water, but in a later shot through a window, the plug and hole are gone.
Continuity mistake: If you look carefully, you will notice that on the title sequence, patchy the pirate's eyepatch changes eyes. This varies from episode to episode.
Suggested correction: The eyepatch doesn't change position from episode to episode. You must be thinking of "Christmas Who?" where Patchy accidentally hits himself in the eye with his hook. And the pirate from the theme song's name is Painty the Pirate. Patchy and Painty are two completely different characters.
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.
Your Shoe's Untied / Squid's Day Off - S2-E2
Continuity mistake: In "Your Shoes Untied", when he is in the Krusty Krab kitchen. In between shots when Squidward keeps asking Spongebob to give him the Krabby Patty, the patties on the grill disappear and reappear between shots.
Mermaid Man and Barnacle Boy III / Squirrel Jokes - S2-E4
Continuity mistake: Before he comes on his second act, there is a front shot of the crowd, you see a guy in the front with his hands up, but in the next shot, which is of his back, his hands are down.
Sandy, SpongeBob and the Worm / Squid on Strike - S2-E18
Continuity mistake: In Spongebob, Sandy and the Worm, when Sandy ties the worm's tongue in a knot and they run from the worm, the worm opens it's mouth but you don't see the tongue tied in a knot.
No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: In "No Weeneis Allowed", Patrick punches SpongeBob's left eye, but the black eye is on SpongeBob's right eye.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: In The Snowball Effect, Squidward builds his fort between his and Spongebob's house later in the ending scene his fort has moved about 30 yards away.
Grandma's Kisses / Squidville - S2-E9
Continuity mistake: Spongebob's watch appears and disappears between shots.
The Great Snail Race / Mid-Life Crustacean - S3-E15
Continuity mistake: In The Great Snail Race, Gary wipes out into the tires then fire fighters come and put him out (still near the tires) but in the wide shot Gary is back on the track.
Your Shoe's Untied / Squid's Day Off - S2-E2
Continuity mistake: At the beginning of "Squid's Day Off", There is a tiny bell painted gold sitting on the opening between the kitchen and restaurant. When the shot changes, the bell disappears, then reappears when the shot changes again.
The Chaperone / Employee of the Month - S1-E12
Continuity mistake: Spongebob absorbs the pink punch making him look pink in 2 shots - one showing him squirting punch out of his nose, but a shot after that shows him yellow.
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.
Boating Buddies/The Krabby Kronicle - S6-E9
Continuity mistake: In "Krabby Kronicle," when the female fish takes a copy of The Bottom Feeder, the pile of newspapers stays the same.
SpongeBob's House Party (aka Party Pooper Pants) - S3-E10
Continuity mistake: When Gary and Spongebob are waiting at the door, there is a sign behind him that says "pin the tail on the horace" (yes it says horace), and there is one tail hanging up, but when everybody comes in there are suddenly two.
Pre-Hibernation Week / Life of Crime - S2-E13
Continuity mistake: When his pants fall off when he's trying to hide, his pants are hooked to the plant by the brown part of his pants, but when Sandy comes looking and she sees his pants on the plant, they're hooked by the white part.
Grandma's Kisses / Squidville - S2-E9
Continuity mistake: When Squidward enters Squidville, he is looking for apartment number 304. When he is looking for his apartment, the numbers on the doors disappear and re-appear.
Survival of the Idiots / Dumped - S2-E8
Continuity mistake: When the winter ends, there's a shot of Sandy's tree, and there's no window in it. When Sandy sees SpongeBob and Patrick, suddenly the tree has a window. A very noticeable mistake.
Grandma's Kisses / Squidville - S2-E9
Continuity mistake: When SpongeBob and Patrick had used the reef blower to take parts of Squidward's house off, they had taken off all parts but the two ear-like parts on the sides of the house. When Squidward demands that they put the parts back, the ear parts are no longer on the house, but are being blown back onto the house. This isn't possible because they were never taken off in the first place.
Pre-Hibernation Week / Life of Crime - S2-E13
Continuity mistake: When Spongebob and Patrick have run away, when they are fighting about the chocolate, Patrick has chocolate all over his mouth. Patrick says something like "I'll get there first" and starts running after Spongebob, and in the next shot his face is completely clean.