Continuity mistake: In the scene where SpongeBob has given his pants to the clam, two continuity errors appear. First, Patrick puts his head in the pants and he says that the clam is hungry. A lot of holes are in his head. In the very next shot, the holes are gone. This is really obvious. The other continuity error is that before Patrick gets those holes, SpongeBob isn't with his pants. When he tries to give the Patty to the clam, he's suddenly with his pants, when the little clam is supposed to have his pants.
Continuity mistake: In "Rock-a-Bye Bivalve," near the end, the timecard says it's midnight and it is dark outside. However, when the bivalve flies away, it's morning (judged by the shadows of the houses, even late morning), even though just a few minutes passed.
Continuity mistake: In "Rock-a-Bye Bivalve" when Spongebob and Patrick hear the bivalve chirping, the coral that vibrates is bright green and is standing up straight. However, when they find the bivalve and take it out from behind the coral, the coral is dark green and is bent over.
Revealing mistake: In the shot that shows the outside of the Krusty Krab (in Krab Borg) they reused the drawing of right before the customers ran out of the building because you can see many customers crowded at the door. This shot lasts about 2 seconds but it's not hard to spot.
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.