No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: When Squidward has sort of a strict conversation with Spongebob, Mr. Krabs, and later Patrick, the 3 of them he was talking to, were side by side, but a shot later, Mr. Krabs and Spongebob are side by side, but farther from Patrick.
The Sponge Who Could Fly (aka The Lost Episode) - S3-E16
Continuity mistake: After the walk cycles, the color bars change between shots.
Nasty Patty / The Idiot Box - S3-E4
Continuity mistake: In the scene where Spongebob and Mr. Krabs bury the health inspector, Spongebob buries him so that way his head is above ground covered by a pile of dirt. In the next shot of the buried health inspector, he is buried horizontally.

Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: In the scene where the guard pulls Mrs. Puff out of the rock yard, her hat is red, then blue, then red again throughout the cuts in the scene.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: In One Krabs Trash, Spongebob pays Mr. Krabs with what looks like two dollars, which should have been five, and when he comes back he has two dollars that doubles into four in the next shot of him leaving.
The Graveyard Shift / Krusty Love - S3-E13
Continuity mistake: When Squidward sees the "ghost", he gets so frightened that hair comes out of his head and his job's hat falls off. In the very next shot, the hair is gone, and the hat is there again.
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: In the episode Welcome to the Chum Bucket, when Plankton is reading a story to SpongeBob, he is interrupted. When he looks up and sees SpongeBob asleep, Sponge doesn't have his Chum Bucket Bucket Helmet on. When Plankton decides not to hit SpongeBob with a mallet and wakes him up, Sponge has the helmet on again.

Chocolate With Nuts / Mermaid Man And Barnacle Boy V - S3-E11
Revealing mistake: In one scene with Spongebob, Patrick, an old lady, and her almost dead mom, in one part Spongebob has no holes on his face. There is also a light-colored spot near Patrick's mouth.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: In the scene where, Squidward accidentally squirts lemon juice in his eye it goes in his right eye but he squints with his left eye.
Suggested correction: In "The Snowball Effect", Squidward squirts the lemon wedge's juice into his left eye and he closes his left eye. There is no continuity error.
Wet Painters / Krusty Krab Training Video - S3-E9
Audio problem: When Mr. Krabs comes back to his house, he eventually encounters a stack of 11-12? pictures, but we only hear him take 5 or so before he runs into Spongebob.
Nasty Patty / The Idiot Box - S3-E4
Audio problem: When SpongeBob and Patrick give Squidward the T.V, Squid's mouth doesn't move when he says "Oh boy, oh boy, oh boy!"
SpongeBob's House Party (aka Party Pooper Pants) - S3-E10
Continuity mistake: Patchy's hook hand disappears when he is playing the accordian.
Nasty Patty / The Idiot Box - S3-E4
Continuity mistake: In "Nasty Patty," just before Spongebob goes around the back of the Krusty Krab, the sign is on the right and it is electric. In every other episode, it is painted and on the left.
The Great Snail Race / Mid-Life Crustacean - S3-E15
Continuity mistake: When SpongeBob runs to help Gary in the race, Patrick's "snail" has disappeared.
The Sponge Who Could Fly (aka The Lost Episode) - S3-E16
Continuity mistake: When the parrot lands the egg on the remote, in the next shot it vanishes.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Continuity mistake: At the beginning of "Born Again Krabs", it shows the outside sky being orange-ish. But when it shows SpongeBob and Mr. Krabs talking about the old patty, you can see a little blue crack through the window.

SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Other mistake: Pranks a Lot: When everyone is cheering on Spongebob and Patrick at the end, Sandy whistles by putting her hand through her helmet. Impossible. (00:23:30)
Krab Borg / Rock-a-Bye Bivalve - S3-E8
Revealing mistake: In the shot that shows the outside of the Krusty Krab (in Krab Borg) they reused the drawing of right before the customers ran out of the building because you can see many customers crowded at the door. This shot lasts about 2 seconds but it's not hard to spot. (00:08:05)
The Algae's Always Greener / Sponge Guard On Duty - S3-E7
Continuity mistake: In "The Algae's Always Greener", after Squidward barges into Mr. Plankton's office, you can see that there are no krabby patties on Mr. Plankton's desk, but when it pans back to Mr. Plankton's desk, there are two krabby patties on his desk. (00:07:35)
SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Revealing mistake: In "Spongebob Meets The Strangler" when that fish holds up Spongebob's dry cleaning at the supermarket, it looks like he is holding it up with a coathanger because his hand is up in the air, but you can easily see nothing is holding it up. It's just floating up in the air.
Suggested correction: The clothes are being held up by a coat hanger. It may be hard to see due to it blending in with the wall color, but if you look closely, it's there.