Krab Borg / Rock-a-Bye Bivalve - S3-E8
Continuity mistake: In 'Rock-a-Bye Bivalve' Spongebob's front door changes hinge sides. Also at the end suddenly there's a light switch next to the door which wasn't there earlier.
The Secret Box / Band Geeks - S2-E14
Continuity mistake: In Band Geeks on day four the lever besides the big gate changes positions between pointing upwards and downwards several times.
Help Wanted / Reef Blowers / Tea at the Treedome - S1-E2
Revealing mistake: In the shot where Spongebob says, "That little squirrel is in trouble, " half of his belt is missing.
The Secret Box / Band Geeks - S2-E14
Continuity mistake: When the band is marching through the streets, whilst Squidward is pressuring the flag twirlers to move faster, there are some fish drumming behind them. One is a blue fish wearing a yellow shirt seen standing on the left, and another is a brown fish wearing a red shirt seen standing on the right. When the flag twirlers behind to fly off the ground, those two fish have swapped places.
Mermaid Man and Barnacle Boy / Pickles - S1-E6
Other mistake: In the end credits for the episode "Pickles", Bubble Bass is named "BubbleBass" (without a space).
Mermaid Man and Barnacle Boy III / Squirrel Jokes - S2-E4
Revealing mistake: When we see Billy get told about the stupid squirrel, he has a sleeve going through his arm. The moment he starts talking, the sleeve disappears and his arm extends over his shirt. Around the end of the shot when he's being pulled away, the sleeve returns.
Character mistake: In "Sandy's Nutty Nieces" SpongeBob gets thrown and flung at Sandy's treehouse, then when he falls down and Sandy opens the door, SpongeBob's shirt color changes. (00:01:25)
Rise and Shine / Waiting / Sing a Song of Patrick - S5-E1
Factual error: As Patrick's song causes havoc, two airplane pilots deserts the airplane and deploy their parachutes. The issue with this is that the two pilots should have come to a stop relative to the airplane's movement.
Roller Cowards / Bucket Sweet Bucket - S5-E8
Deliberate mistake: In 'Bucket Sweet Bucket' there's no way that Plankton managed to reach with his paint brush to repaint the entire front of his establishment from the top of Squidward's head.
Plot hole: After being spared, Medieval Sandy announced that she will help in the defeat of medieval Plankton. How did she know what they were planning?