SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Plot hole: In "Pranks A Lot", Patrick and SpongeBob scare Sandy. When Sandy runs, gets into her rocket and flies away. When she moved bubbles appeared meaning there's water in her tree house. There's no water in there in other episodes because she's a land animal and breathes air.
SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Plot hole: When the invisible Spongebob and Patrick scare Sandy, they are using a sheet to appear as "ghosts". However, the form of the sheet reveals that they don't have their helmet bowls on. How could they survive in the treedome that time? They sounded fine, not dehydrated.
Club SpongeBob / My Pretty Seahorse - S3-E12
Revealing mistake: In Club SpongeBob, when SpongeBob, Patrick and Squidward are in the forest, Squidward asks the magic conch shell if he can have something to eat. Straight after he asks "Can't you say anything else but 'No'?", it has a close-up of the shell. But Squidward's arm appears to be yellow, like SpongeBob's. This error was later corrected in 2019 when the episode was remastered for digital releases.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Plot hole: In "Mermaid man and Barnacle Boy", Plankton is shown as taller than the town at the end of the episode. However, when Spongebob is shrinking the people of Bikini Bottom, their sizes in the pickle jar seem to be equal with Plankton's actual height. In reality, Plankton should have been around the same size as the rest of Bikini Bottom's residence after the shrinking, not 5 times taller.
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.
The Snowball Effect / One Krabs Trash - S3-E3
Character mistake: When Mr. Krabs sees the headstone, it says SmittyWerbenManJensen and not SmittyWerbenYaegerManJensen.
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.
Answer: I believe this is the Season 6 episode "Spongicus".