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.
SpongeBob Meets the Strangler / Pranks a Lot - S3-E20
Continuity mistake: In Spongebob Meets The Strangler, the Tattletale Strangler's dots on his head change numbers constantly. Sometimes there are 5 on his right, sometimes 6, sometimes his left side has a scar and 5 dots, sometimes a scar and no dots.
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.
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.
Krab Borg / Rock-a-Bye Bivalve - S3-E8
Continuity mistake: In "Rock-a-Bye Bivalve," near the end, the timecard says it's midnight and it is dark outside. However, when the bivalve flies away, it's morning (judged by the shadows of the houses, even late morning), even though just a few minutes passed.
SpongeBob's House Party (aka Party Pooper Pants) - S3-E10
Continuity mistake: When Patchy the Pirate is flying through the houses, he finally hits a pole with nothing on him. Yet when Patchy comes screaming back into his hat, he had a broken window in him and wood through his hat.
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.
Nasty Patty / The Idiot Box - S3-E4
Continuity mistake: When SpongeBob and Mr.Krabs are dragging the health inspector up the hill he doesn't have his hat on, but when he gets hit by the rock his hat is on.
Continuity mistake: Gary leaves big saliva trails. When Squidward realizes that Gary leaves these saliva trails, we can see that is a trail in front of Squidward's house. When Squidward tells SpongeBob about these trails in the language of the past, we can see that the trail of the saliva has changed: it bigger and almost in all the scenery. After a while, we see that the road goes directly to Squidward's house, to its door. How did the road change, if we haven't seen Gary moving?
No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: In "No Weeneis Allowed", Patrick punches SpongeBob's left eye, but the black eye is on SpongeBob's right eye.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: In The Snowball Effect, Squidward builds his fort between his and Spongebob's house later in the ending scene his fort has moved about 30 yards away.
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.
SpongeBob's House Party (aka Party Pooper Pants) - S3-E10
Continuity mistake: When Gary and Spongebob are waiting at the door, there is a sign behind him that says "pin the tail on the horace" (yes it says horace), and there is one tail hanging up, but when everybody comes in there are suddenly two.
No Weenies Allowed / Squilliam Returns - S3-E6
Continuity mistake: In "Squilliam Returns", the world's smallest violin changes position between shots.
As Seen on TV / Can You Spare a Dime? - S3-E5
Continuity mistake: In "As Seen On T.V", the hat on Mr. Krabs's desk has 2 lines on the anchor instead of 1.
Krab Borg / Rock-a-Bye Bivalve - S3-E8
Continuity mistake: In Rock-a-Bye Bivalve, Spongebob's tie turns black when he is doing the chores on Patrick's second day of work, and then turns back to normal when he walks into the living room.
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.
The Algae's Always Greener / Sponge Guard On Duty - S3-E7
Continuity mistake: When Plankton says, "Look at his daughter. She's as big as a whale!", the soda can on the table suddenly moves to the left.
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.
Answer: I believe this is the Season 6 episode "Spongicus".