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.
Plot hole: As Spongebob is trying to let the Jellyfish out of their enclosure after discovering what Mr Krabs is doing to them, Krabs says, "That door will only open if I say...open." Then he suddenly realises what he's said and the door opens. How come the door didn't open when in his sentence he first said open? The door didn't activate itself until he said open the second time.
Plot hole: In the end of "Pranks A Lot" SpongeBob and Patrick glue the door shut in order to keep Mr. Krabs inside the Krusty Krab. When SpongeBob And Patrick are visible again, it turns out that a lot of customers have entered the Krusty Krab to see SpongeBob and Patrick naked. All of those people had no way to get into the Krusty Krab with the doors glued shut. It can't be that they broke down the doors, as they're still there.
Plot hole: In MuscleBob BuffPants, when SpongeBob first shows off his new inflatable muscles to everyone on the beach, he had the strength to punch two muscular fish into the air with them. A minute later, he could not even lift a glass of juice with the inflatable muscles.