Continuity mistake: In "Mermaidman Begins", Mermaidman and Barnacleboy are running across a dock, about to jump into the sea. Next to them, on the right, there is a pelican sitting on a pillar. In the next shot at a different angle, the pelican is gone.
Continuity mistake: In "A Flea in Her Dome", Patrick asks Spongebob to get on Sandy's shoulders. Then, he climbs onto Spongebob's shoulders. In the next shot, they are suddenly next to Sandy's tree.
Continuity mistake: In "The Krusty Plate", Spongebob finds that one plate has a brown smudge on it. After an attempt to clean the plate, he lifts it up and the smudge is now a light shade of green.
Continuity mistake: In "A Flea in Her Dome", Patrick gets bitten by a flea and his chest is covered in bites. He takes out a pencil and connects some of the dots to make a horse. A few shots later, the horse and the bites disappear.
Continuity mistake: In "Giant Squidward", Squidward goes to spray his wilting kelp with fertilizer and sets down a watering can right next to him. When the kelp goes back to normal in the next shot, the watering can disappears and is not seen again.
Continuity mistake: In "Hall Monitor" when SpongeBob is pretending to be the "open window bandit," you can see a red piece of coral outside of the house that he is about to break in to. When he jumps through the open window, frightens the people inside, and they run out of the house, the red piece of coral is gone.
Continuity mistake: In "Jellyfishing" when Squidward comes home in the bed thingy, the king jellyfish hovers above him. At first, Squidward is facing his house. But in the next shot, he is facing the road. When he replies "Ow" he is facing his house again.
Continuity mistake: The scene in episode Rock-a-Bye Bivalve where SpongeBob and Patrick start arguing about working for Junior at Patrick's house, SpongeBob is not inside the house. While SpongeBob is staring down at Patrick, his head is sticking out of the top of the hole in the ground. Once SpongeBob jumps in the top of the hole is way past their head.
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.