SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Continuity mistake: When The Strangler and Spongebob arrive at the pineapple, look at the door: there is no doormat below it, but a couple minutes later Spongebob pulls a key out from under the doormat that was not there before.
SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Continuity mistake: In "Pranks-A-Lot" when Sandy flies out of her dome in an escape pod to Texas, she leaves a big hole on top of her dome. In the next shot, it's gone. Very noticeable mistake.
Continuity mistake: In the episode "Missing Identity", when Spongebob is talking to Patrick about saying "hi" to him the first time, Squidward's house is gone.
The Great Snail Race / Mid-Life Crustacean - S3-E15
Continuity mistake: When Gary explodes or breaks down (or something like that), Snellie, Squidward's snail, rushes over to Gary. At first you see the track but the next shot (really quick) you don't see it.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: On "One Krab's Trash", when Mr. Krabs draws a ghost on a sheet of paper, it shows before it goes into Spongebob's rooms that there's only writing on one side (i.e. the ghost) and when it goes into his room, a shopping list is on the back.
No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: In "No Weenies Allowed", the gatekeeper in front of the sailor club has a tattoo on his front with a heart and MOM on it. Sandy rips it out and places it back upside down. It now shows an upside down heart with WOW. In the next cuts between this and when Spongebob gets sent to the Weenie place, the tattoo suddenly has the heart downside up reading WOW, or upside down reading MOM. This is never possible because MOM was supposed to be with the downside up heart, not the upside down heart.
The Graveyard Shift / Krusty Love - S3-E13
Continuity mistake: In "The Graveyard shift", Squidward begins to count the signals that means the ghost will appear. "First the lights, then the phone.", and a green slime appears in the wall. Squidward says "Oh, wait, they always do that, but what was the third thing?", and the bus appears at the front of the Krusty Krab. SpongeBob says, "I didn't know the bus comes here at this hour", and look at the wall: the green slime has disappeared.
SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Continuity mistake: In "Pranks A Lot": SpongeBob and Patrick are going to burn Mr. Krab's dollar, so he throws water on them and they become visible. Patrick is holding Mr. Krab's dollar. When he says "We're visible again", and he and SpongeBob start to scream, the dollar completely disappears.
SpongeBob's House Party (aka Party Pooper Pants) - S3-E10
Continuity mistake: When Spongebob comes home after being arrested, he picks a spare key up from under his mat and gets angry at himself for trying to break in the night before. When he walks in, discomfort on his face, the mat is gone.
The Great Snail Race / Mid-Life Crustacean - S3-E15
Continuity mistake: When Gary was spinning out of control, there were at least 5 lanes on the track but before there were only 3.
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.
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.
Answer: I believe this is the Season 6 episode "Spongicus".