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.
Continuity mistake: In the episode "Plankton's Army", there is a group of Plankton's family sitting on top of the toilet when Mr. Krabs is first shown inside it. In two shots, the group has vanished from the top of the toilet.
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.
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.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: At the start of MMIV, SpongeBob rips off a person's pocket to get a pen. He totally rips it off, but none of the pocket's material is visible later.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: In MMIV, there is no phone next to the door when SpongeBob shrinks the pickles. Later, Squidward calls on a phone.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: At the start, when Mermaid Man and Barnacle Boy run out of the Krusty Krab there are cars everywhere. When SpongeBob runs to try and get Mermaid Man's autograph inside the Krusty Krab there are no cars visible.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: Mermaid Man and Barnacle Boy IV: When SpongeBob runs into the kitchen with Mermaid Man's secret utility belt, the door swings open facing away from the grill, but when Squidward demands to know what's going on in the kitchen, the door opens the opposite way.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: In "Doing Time", Spongebob's entire face fills the chili bucket, but when he peeks out, his body is relatively smaller than the bucket.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: When SpongeBob zaps the pickles, he is standing next to the door. He instantly moves to the center of the room in a subsequent shot.
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: Frankendoodle: When SpongeBob pranks Squidward by pulling the dollar away from him, Squidward's monocle falls on the ground, but when the mustache flies away, the monocle has vanished. A chain on the monocle also appears in one shot, then disappears. (00:15:47)
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: Frankendoodle: When DoodleBob first starts beating up Squidward, the door to Squidward's house is open, but two shots later, the door has completely vanished. (00:16:32)
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.
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.
Welcome to the Chum Bucket / Frankendoodle - S3-E2
Continuity mistake: In 'Welcome to the Chum Bucket', the sky is constantly changing in an abnormal way. First, it is daylight when Plankton takes Spongebob into the Chum Bucket. When Spongebob starts singing, the sun is either coming up or going down. When Mr. Krabs starts singing, look through the hole in the wall and the sky looks to be about afternoon. When Spongebob and Mr. Krabs finish their song, it's nighttime.
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.
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.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: In "One Krab's Trash," after SpongeBob discovers the drinking hat at Mr. Krabs' yard sale, the two straws are connected to a cylinder with a hole. But when Mr. Krabs says "You were born to wear this hat!" the little cylinder has vanished. Later when SpongeBob is blowing bubbles, the cylinder has reappeared. (00:02:25 - 00:05:00)
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.
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".