Squidtastic Voyage/That's No Lady - S4-E15
Continuity mistake: In "That's No Lady", Squidward is standing at the register, holding a newspaper. When it cuts to "Patricia", and back to Squidward, Squidward isn't holding the newspaper anymore.
Skill Crane/Good Neighbors - S4-E4
Continuity mistake: In "Good Neighbors", Squidward stomps on Spongebob and Patrick's fezzes in front of his door. Then, it cuts to a shot of Squidward's house, but the fezzes are gone.
Help Wanted / Reef Blowers / Tea at the Treedome - S1-E2
Continuity mistake: The office door in the Krusty Krab is missing throughout the episode.
Suggested correction: It's a pilot episode. Things can change with a show when it gets picked up into a series.
House Sittin' for Sandy/Smoothe Jazz at Bikini Bottom - S8-E23
Continuity mistake: When Sandy finds SpongeBob and Patrick after wrecking the tree dome, the distance between SpongeBob/Patrick and Sandy changes constantly between shots.
Back to the Past/The Bad Guy Club for Villains - S7-E16
Continuity mistake: The Quickster was a member of the I.J.L.S.A in Mermaid Man and Barnacle Boy V. But in this episode, there isn't The Quickster in the I.J.L.S.A, but instead the Pi-Right Ponderer.
Fear of a Krabby Patty/Shell of a Man - S4-E1
Continuity mistake: When Mr. Krabs drags SpongeBob back into the kitchen, Squidward's facial expression changes between shots.
Karen 2.0/InSPONGEiac - S8-E28
Continuity mistake: Karen dumps a load of chum on a tray and some of the chum lands on the table. The chum that fell on the table magically disappears from shot a split second later.
Continuity mistake: When SpongeBob and Patrick see the map, a compass is seen next to it. As the two start touching the map, the compass has disappeared.
The Krabby Patty That Ate Bikini Bottom/Bubble Buddy Returns - S8-E15
Continuity mistake: The giant Krabby Patty eats SpongeBob's shoe and sock in the kitchen. But by the time SpongeBob and Squidward run to the door and are stopped by Mr. Krabs, the shoe and sock have magically reappeared.
Dying For Pie / Imitation Krabs - S2-E6
Continuity mistake: SpongeBob makes Squidward a tear jumper and there is a shot of Squidward sighing. In this shot, we can see no-one standing around the register. In the next shot, Mr. Krabs has suddenly appeared next to it.
As Seen on TV / Can You Spare a Dime? - S3-E5
Continuity mistake: When SpongeBob is making the patties at the end, he puts at least 20 patties on the grill. But just after he takes the buns out of the bag there are now only 10 patties.
Mermaidman Begins/Plankton's Good Eye - S8-E22
Continuity mistake: When Plankton tries to open the safe, his arms come off. The arms stay on the safe. But when Mr. Krabs approaches the safe in the next shot, Plankton's arms have disappeared from the safe.
You Don't Know Sponge/Hide and Then What Happens - S8-E3
Other mistake: It is revealed in this episode that Patrick is right-handed. However in the episode "Krusty Towers", when asked to sign the Krusty Towers guest register, he is shown doing so with his left hand.
The Snowball Effect / One Krabs Trash - S3-E3
Continuity mistake: In "One Krab's Trash," after SpongeBob discovers the drinking hat at Mr. Krabs' yard sale, the two straws are connected to a cylinder with a hole. But when Mr. Krabs says "You were born to wear this hat!" the little cylinder has vanished. Later when SpongeBob is blowing bubbles, the cylinder has reappeared. (00:02:25 - 00:05:00)
Mermaid Man and Barnacle Boy IV / Doing Time - S3-E1
Continuity mistake: When SpongeBob zaps the pickles, he is standing next to the door. He instantly moves to the center of the room in a subsequent shot.
Chocolate With Nuts / Mermaid Man And Barnacle Boy V - S3-E11
Continuity mistake: After MermaidMan screams "To Make Out Reef" he accidentally falls over on his chair. When Patrick complains that they aren't gonna get pizza the chair is back up again.
Culture Shock / F.U.N. - S1-E10
Continuity mistake: When we first see Squidward in the canyon background, his outlining is gone. Then, in the next shot, it's back.
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.