The Algae's Always Greener / Sponge Guard On Duty - S3-E7
Continuity mistake: The Algae's Always Greener: After Plankton uses his machine and wakes up in the Krusty Krab office, he looks out through the porthole on the office door leading to the eating area, but the porthole on that office door vanishes when Plankton returns to the office with the two Krabby Patties. (00:04:25)
The Snowball Effect / One Krabs Trash - S3-E3
Other mistake: In 'The Snowball Effect' when Squidward attempts to make Patrick and Spongebob resume their snowball fight he throws a snowball at them which they avoid, and it puts out Squidward's fire inside. Squidward had his back towards his house and threw the snowball in the opposite direction.
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: The pencil's length in 'Frankendoodle' varies in between above and beneath the water surface.

Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Other mistake: When the citizens pop out of Sponge Bob's holes near the end of Mermaid Man and Barnacle Boy 4, if you look closely, Sandy's head is gone except her eyes and nose.
Chocolate With Nuts / Mermaid Man And Barnacle Boy V - S3-E11
Continuity mistake: When Barnacle Boy and E.V.I.L. are hiding behind the rock you can see Barnacle Boy's fingers. In the next shot he is wearing gloves.
Krab Borg / Rock-a-Bye Bivalve - S3-E8
Continuity mistake: In "Rock-a-Bye Bivalve" when Spongebob and Patrick hear the bivalve chirping, the coral that vibrates is bright green and is standing up straight. However, when they find the bivalve and take it out from behind the coral, the coral is dark green and is bent over.
The Great Snail Race / Mid-Life Crustacean - S3-E15
Continuity mistake: When Squidward looks through a window of SpongeBob's house, Patrick looks through a higher window. An outside shot shows that Patrick is standing in Squidward's shoulders, however, an inside shot shows that Patrick isn't in Squidward's shoulders.
SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Plot hole: In the end of "Pranks A Lot" SpongeBob and Patrick glue the door shut in order to keep Mr. Krabs inside the Krusty Krab. When SpongeBob And Patrick are visible again, it turns out that a lot of customers have entered the Krusty Krab to see SpongeBob and Patrick naked. All of those people had no way to get into the Krusty Krab with the doors glued shut. It can't be that they broke down the doors, as they're still there.
Suggested correction: Mr. Krabs most likely washed the glue off the doors and let the people in.
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Character mistake: In 'Welcome to the Chum Bucket', Spongebob said he likes the grill facing the wall to the right. Plankton pushes it so that it is facing the wrong wall, the wall on the left.
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: At the end of "Welcome To The Chum Bucket", look at Spongebob's eyes. His eyebrows are more far apart than usual, also his eyeballs are uneven a bit.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Audio problem: At the end of "Born Again Krabs", SpongeBob is talking to The Flying Dutchman on the phone. SpongeBob's dialogue isn't in sync with his mouth.
Nasty Patty / The Idiot Box - S3-E4
Continuity mistake: In "The Idiot Box", Spongebob and Patrick are standing on the curb of the street and there is a building in the distance. Several shots later, they are standing in the same spot, but the building has disappeared.
As Seen on TV / Can You Spare a Dime? - S3-E5
Revealing mistake: When SpongeBob is mopping the floor, two kids walk into the background and put mustard and ketchup on their patties. Nothing is coming out of the condiment tap.
No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: At the beginning of "Squilliam Returns," Squilliam is walking to Squidward from the left of the garbage pails. When Squidward throws his hat out, Squilliam is to the right of the garbage pails.
No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: In "No Weenies Allowed," when Spongebob gets punched by Patrick, he doesn't have a black eye. When the shot zooms to Spongebob's face, he has a black eye.
The Snowball Effect / One Krabs Trash - S3-E3
Character mistake: In the beginning of "One Krabs Trash" Spongebob only has one bill in his hand, a 5 dollar bill. When he goes to his house and comes back, he says he found 68 cents. Therefore, he has 5 dollars and 68 cents. However, he has two dollar bills and a few pennies in his hand, which cannot be made into $5.68.
Chocolate With Nuts / Mermaid Man And Barnacle Boy V - S3-E11
Character mistake: Chocolate With Nuts: When Spongebob and Patrick go to the first house, Spongebob tells the man, "Good afternoon, sir." When they go to the second house, he says, "Good morning, sir." (00:02:52)
New Student Starfish / Clams - S3-E14
Continuity mistake: New Student Starfish: Spongebob shows Patrick the Good Noodles board when they enter the classroom. Then when Patrick is trying to tell the class his name, the number of stars on it change, and the name "Rich" appears on it, which wasn't there before. Later on, when Spongebob and Patrick are in detention, the names on the board are completely different in some shots. (00:02:48 - 00:11:24)
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.