Hooky / Mermaid Man and Barnacle Boy II - S1-E20
Continuity mistake: In "Hooky", Spongebob is being pulled by the hook and grabs onto a flower to try and hold onto it and it becomes limp. In the next shot, this limp flower he just grabbed has vanished.
Krabby Land / The Camping Episode - S3-E19
Other mistake: In "Krabby Land", Mr. Krabs as "Krabby The Clown" finishes his short speech and goes into his office. When he slams the door, bubbles float up and those bubbles stay motionless in the air for a few frames.
Krabby Land / The Camping Episode - S3-E19
Continuity mistake: In "The Camping Episode", Squidward sets down a blanket to lay under the stars and in a couple of shots, the blanket disappears.
Krabby Land / The Camping Episode - S3-E19
Continuity mistake: In "Krabby Land", Spongebob goes to check his motivational quote and from far away, the page is flipped up. But in the next shot, it is a close up and the page is flat against the stack. In the following shot, the page is flipped up again.
Pizza Delivery / Home Sweet Pineapple - S1-E5
Continuity mistake: In "Home Sweet Pineapple", Spongebob goes into Squidward's house to spend the night and sits in his bed with the pillow just the right size for him. But in the next shot, when Squidward climbs into bed next to him, the pillow has drastically grown and now both of them can lay on it perfectly.
Jellyfishing / Plankton! - S1-E3
Continuity mistake: In "Jellyfishing", Patrick and Spongebob slide down two ropes and burn their hands on them. The two shots after they land show them trying to cool down their hands and in the shot after that, the ropes they had just slid down on have disappeared.
Pizza Delivery / Home Sweet Pineapple - S1-E5
Continuity mistake: In "Pizza Delivery", Spongebob points out the antennae for the boat during his vehicle inspection, but in a few shots, when he's checking the tire pressure, the antennae has vanished.
Born Again Krabs (aka A Penny Saved) / Safety Freak (aka I Had An Accident) - S3-E17
Continuity mistake: In "I Had An Accident", Sandy opens the door to show that she was being "attacked" by a gorilla and Spongebob is looking through that door to see the events unfold. But after a couple of shots, the door has closed by itself and Spongebob has to open it again before going outside.
SB-129 / Karate Choppers - S1-E14
Continuity mistake: In "SB-129", every time Squidward goes to answer the door to find Spongebob and Patrick there, the picture on the wall next to the door changes noticeably.
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.
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?