The Graveyard Shift / Krusty Love - S3-E13
Continuity mistake: In 'The Graveyard Shift' Squidward explains that there are three signs concerning the arrival of the Hash-Slinging Slasher. He then holds up three hands. In the next shot, he is only holding up one hand.
The Graveyard Shift / Krusty Love - S3-E13
Continuity mistake: Graveyard Shift - Sometimes the kitchen walls are light green, and sometimes they are dark green.
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)
New Student Starfish / Clams - S3-E14
Continuity mistake: In the episode New Student Starfish., SpongeBob's good noodle stars changes number throughout the 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".
New Student Starfish / Clams - S3-E14
Continuity mistake: When Spongebob shows Patrick the good noodles chart all the stars are wildly scattered in each row. When Patrick is trying to announce his name to the class they're all in a neat row. When Mrs. Puff is removing the star from Spongebob's row they're scattered again.
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 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.
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 Great Snail Race / Mid-Life Crustacean - S3-E15
Continuity mistake: Gary crashes to a tire. After a while you see the tire is gone. Also, Gary stayed in the right of the track, crashed, but when SpongeBob helps him, Gary is in the middle of the track.
The Great Snail Race / Mid-Life Crustacean - S3-E15
Continuity mistake: When Patrick and Squidward stick their heads through the windows of Spongebob's house, on the outside you can see that they're next to the front door. But from the inside, their heads are next to a totally different door.
The Great Snail Race / Mid-Life Crustacean - S3-E15
Continuity mistake: In The Great Snail Race, Gary wipes out into the tires then fire fighters come and put him out (still near the tires) but in the wide shot Gary is back on the track.
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.
The Sponge Who Could Fly (aka The Lost Episode) - S3-E16
Continuity mistake: After the walk cycles, the color bars change between shots.
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.
The Sponge Who Could Fly (aka The Lost Episode) - S3-E16
Continuity mistake: On the news one fish had hair. Later it was gone.
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.
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.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Continuity mistake: In "I Had An Accident", Sandy opens the door to show that she was being "attacked" by a gorilla and Spongebob is looking through that door to see the events unfold. But after a couple of shots, the door has closed by itself and Spongebob has to open it again before going outside.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Continuity mistake: In "Born Again Krabs", when Mr. Krabs first makes his appearance next to Davy Jones' locker, there is some coral taking up a part of the bottom left corner. In a few shots, that same set of coral has disappeared.
Answer: I believe this is the Season 6 episode "Spongicus".