Continuity mistake: In the live-action pirate beginning, between a wideshot and closeup, the sky changes from grey/overcast to bright blue with fluffy white clouds. (00:01:15)
Continuity mistake: In SpongeBob's dream, the Krabby Patty moves all around the table several times. First it's in the center, then near the edge, and then near SpongeBob. (00:03:40)
Continuity mistake: Spongebob puts his shirt/shorts clothing on after his dream, and he is wearing underwear. Then, in front of the mirror, when the back of the shorts falls down, it shows his rear end with no underwear. (00:05:15)
Continuity mistake: Spongebob steps on Plankton, then wipes his shoe, leaving a big green smear on the road. In the following shot it's gone. (00:09:25)
Continuity mistake: In the courtroom scene with King Neptune, Mindy's gold band keeps disappearing and reappearing. (00:13:20 - 00:14:55)
Continuity mistake: In the Goofy Goober Nut Bar, the pictures hanging on the wall behind Spongebob change in every shot. (00:15:55)
Continuity mistake: When SpongeBob is first shown crying at the Nut Bar, you can only see one row of chairs. When SpongeBob gets up to leave, there is now a corner and another row. (00:16:30 - 00:17:30)
Continuity mistake: When Spongebob wakes up the morning after his ice cream antics at Goofy Goober, there is a table and two chairs by the stage which disappear. (00:18:15)
Continuity mistake: The swirls on the lollipop drunk SpongeBob is holding drastically change between shots. (00:18:35)
Continuity mistake: The distance between the two Krusty Krab restaurants keeps changing throughout the movie. (00:18:45)
Continuity mistake: In the scene where Neptune originally enters the Krusty Krab 2, if you look out the window the original Krusty Krab isn't there. It also isn't there when he says "Have this pole executed." (outside the Krusty Krab 2) (00:19:05 - 00:20:00)
Continuity mistake: When SpongeBob is "drunk" at Goofy Goober's, after the waiter tells him to scoop up his friend, SpongeBob falls flat on his face. In the close up of him, some green ice cream suddenly appears. (00:19:10)
Continuity mistake: The "Galley Grub" sign in Krusty Krab 2 moves from above the door with a porthole in it, to next to the door with the anchor painted on it, and then totally disappears later. (00:21:00)
Revealing mistake: When SpongeBob is telling King Neptune how much of a jerk Mr. Krabs is, when SpongeBob says, "I am 100 percent man," he leans back and you can see his hat is just floating there. (00:22:25)
Suggested correction: If you mean that it stays on his head, you do realise that they are underwater? It would stay on his head.
Even though they're underwater, everything else stays on the ocean floor level. Therefore, the hat shouldn't stay on Spongebob's head. It should fall off it and hit the floor.
Continuity mistake: When SpongeBob is in King Neptune's hands, you can see there are many people in the Krusty Krab. But when Neptune throws SpongeBob on the ground, nearly everyone vanishes. (00:23:30)
Continuity mistake: After SpongeBob and Patrick bust out of the Krusty Krab, it cuts to inside the KK. You can see there's no one at the door, but Plankton appears mid-shot when he opens the door. (00:28:05)
Continuity mistake: When Mr. Krabs is set on fire he runs past once with his clothes, then he runs past in his underwear, then he runs past naked, and jumps into a barrel of water. His clothes are back on. (00:30:05)
Continuity mistake: When we first see Dennis there is writing on his boot but in the next shot it has vanished. (00:32:05)
Continuity mistake: When Spongebob and Patrick go to the bar on the way to Shell City, there is a hole in one of the wooden saloon doors which switches to being in the other saloon door when they sneak out. (00:34:20 - 00:36:00)
Continuity mistake: During the 'Goofy Goober' test at the Thug Tug, the gang leader says "DJ, time for the test!" We see he has a blue hat and glasses before he puts the record on. Later, the gang leader says "DJ! Turn it up louder!" we see that the DJ now has a red/orange hat. (00:35:10)