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.
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.
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.
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.
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.
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.
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.
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.