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.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Continuity mistake: In "Born Again Krabs", after Mr. Krabs returns from the hospital and the Krusty Krab has their "Grand Re-Opening", there are two big yellow signs on the front windows, but in the next shot from the inside, these signs have vanished.
Procrastination / I'm With Stupid - S2-E19
Continuity mistake: In 'Procrastination' when SpongeBob takes the stack of paper out of the drawer, the paper is the only thing in the drawer. In the next shot, SpongeBob pulls a pencil out of the drawer.
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.
Sold!/Lame and Fortune - S9-E21
Continuity mistake: In 'Lame and Fortune', a big box of fortune cookies drops in SpongeBob's backyard. When Gary goes to read his fortune, he leaves a slime trail. However, the slime trail disappears and reappears between shots.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Continuity mistake: In "Born Again Krabs", the doctor taking care of Mr. Krabs drops his clipboard and runs. When the Flying Dutchman appears in the next shot, the clipboard is missing.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Continuity mistake: In "Born Again Krabs", Mr. Krabs drops the coins that the Flying Dutchman gave to him on the floor. In a few shots, when the Flying Dutchman comes back, the coins have vanished.
Grandma's Kisses / Squidville - S2-E9
Other mistake: At the end of Grandma's Kisses, Harold "Bill" is olive green.
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Other mistake: When the citizens pop out of Sponge Bob's holes near the end of Mermaid Man and Barnacle Boy 4, if you look closely, Sandy's head is gone except her eyes and nose.
Chum Bucket Supreme/Single Cell Anniversary - S6-E22
Other mistake: In Chum Bucket Supreme, when Plankton is changing his sign for his restaurant, the door to the Chum Bucket is missing. (00:01:10)
A Pal for Gary/Keep Bikini Bottom Beautiful - S7-E14
Continuity mistake: In "A Pal For Gary", Spongebob opens the door to his library, causing it to fall off its hinges and drop about 5 feet, out of frame. In the same shot, the camera zooms out to reveal that the door is missing.
New Digs / Krabs à la Mode - S5-E6
Continuity mistake: In "Krabs à la Mode", Spongebob is wearing miniature mittens on his eyelashes while walking to the Krusty Krab. They disappear after a few shots.
Squidward's School for Grown Ups - S8-E18
Continuity mistake: Spongebob uses a razor to try and shave off Patrick's beard, which falls onto the ground. In two shots, the razor disappears.
Best Day Ever/The Gift of Gum - S4-E20
Continuity mistake: When SpongeBob tries to steal the gum at night, he's dressed as a bandit, but then the next day when Sandy finds him, he's wearing his normal clothing. He was stuck in the gum all night so there's no way he would have changed.
Continuity mistake: In "The Krusty Drive-through", Mr. Krabs creates a drive-through. However, an updated one can be seen in older episodes.
Karen 2.0/InSPONGEiac - S8-E28
Continuity mistake: In "InSPONGEiac", Spongebob drinks from a glass and drops it on the floor. In two shots, the glass has disappeared.
Continuity mistake: In "Once Bitten", there is a keyhole on one of the doors to the Krusty Krab. Several shots later, the keyhole disappears.
Bubblestand / Ripped Pants - S1-E1
Revealing mistake: In "Ripped Pants", Spongebob plays the guitar and chord changes are heard, but his fingers on the neck of the guitar do not move.
Nature Pants / Opposite Day - S1-E9
Continuity mistake: In "Opposite Day", Spongebob pushes Squidward through the sand, leaving a pile of sand. Two shots later, they are now on Spongebob's sidewalk and the sand pile has disappeared.
Nature Pants / Opposite Day - S1-E9
Continuity mistake: In most of the show, Squidward's house only has windows on the front of his house. But, in "Opposite Day", he has windows on the "ears" of his house, which don't appear throughout the show.
Answer: I believe this is the Season 6 episode "Spongicus".