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.
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)
The Sponge Who Could Fly (aka The Lost Episode) - S3-E16
Continuity mistake: On the news one fish had hair. Later it was gone.
New Student Starfish / Clams - S3-E14
Continuity mistake: In the episode New Student Starfish., SpongeBob's good noodle stars changes number throughout the episode.
The Graveyard Shift / Krusty Love - S3-E13
Continuity mistake: In "Graveyard Shift," when Squidward says to that guy they think is the hash-slinging slasher, "If that was you on the phone and you on the bus, then who was flickering the lights?" look at the "order here" sign. It says "order hear" instead of "order here," which it reads in previous shots during this episode.
New Student Starfish / Clams - S3-E14
Continuity mistake: When SpongeBob and Patrick arrive to the class, SpongeBob writes Patrick's name in the board. Notice that he writes it in capital letters: "PATRICK". After, when Patrick is asked to say his name to the class, and he becomes nervous, look at the board, at Patrick's name: now isn't in capital letters, is normal: "Patrick".
Nasty Patty / The Idiot Box - S3-E4
Continuity mistake: When Mr. Krabs tells Spongebob to make sure the health inspector's head sticking isn't showing, Spongebob's shovel disappears.
SpongeBob's House Party (aka Party Pooper Pants) - S3-E10
Continuity mistake: When Spongebob comes home from the police station in the morning, he gets the spare key from under the mat. That mat definitely wasn't there last night.
The Graveyard Shift / Krusty Love - S3-E13
Continuity mistake: When SpongeBob is cleaning the roof, you can see that there isn't nothing up there. The very next shot shows a closer view to SpongeBob and we can see that is a bucket there. That wasn't there before.
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: Frankendoodle erases the door in SpongeBob's house (when they're fighting in the night). A few moments later you see the door is back.
Chocolate With Nuts / Mermaid Man And Barnacle Boy V - S3-E11
Continuity mistake: When SpongeBob and Patrick are pretending that they need an operation and that fish falls down the stairs, if you look at Patrick's head he has no bandage on his head. But when he looks at SpongeBob right after that fish falls down the stairs, a bandage suddenly appears on his head.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: When mermaid man and barnacle boy are looking for the invisible boatmobile, there are boats all over, even in front of the windows, but when Spongebob is inside running towards the door there are now no boats visible out the window.
Continuity mistake: When Patchy lifts his eye patch to rub his eye and puts the patch on his right eye. In the next shot the patch is on his left eye.
Krab Borg / Rock-a-Bye Bivalve - S3-E8
Continuity mistake: In the scene where SpongeBob has given his pants to the clam, two continuity errors appear. First, Patrick puts his head in the pants and he says that the clam is hungry. A lot of holes are in his head. In the very next shot, the holes are gone. This is really obvious. The other continuity error is that before Patrick gets those holes, SpongeBob isn't with his pants. When he tries to give the Patty to the clam, he's suddenly with his pants, when the little clam is supposed to have his pants.
The Sponge Who Could Fly (aka The Lost Episode) - S3-E16
Continuity mistake: When the tape pours out of the VCR at the end of the show, Patchy the Pirate gets tangled in it. A shot later, the tape is three times longer than it was the shot before it.
No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: In "Squilliam Returns", when Squilliam arrives at the "5-star restaurant" it is nighttime, but at the end when Squidward says "Will you get out of here!" to Mr.Krabs and it zooms out on the Krusty Krab it is daytime.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: In "The Snowball Effect", sometimes Squidward's doorknob is on the left, and sometimes it's on the right.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: In "The Snowball Effect" when Patrick tries to make a snowball the third thing he makes is a DNA strand, if you look closely, when it is in closer, the DNA strand is shorter than when they go out on it.