Continuity mistake: When Mr. Krabs and SpongeBob are standing in front of the bomb after it lands but doesn't go off, the clock inside Mr. Krabs' office can be seen from the kitchen. The time on the clock is 5:00, but in the next shot, the time on the clock is suddenly 3:00. The bomb is then revealed to be a mechanical hand, and the time on the clock is now 5:00 again.
Continuity mistake: When SpongeBob accidentally reveals the location of the formula, Plankton drops the feather he is holding and lands in front of him. The feather remains on the floor, but when Pearl walks into the kitchen, the feather has suddenly vanished, and reappears in front of Plankton in the next shot.
Continuity mistake: When Plankton is telling Karen, "There's a whale in the laboratory," he is jumping up and down with his arms in the air, but in the next shot, his arms are suddenly down at his side.
Continuity mistake: Plankton is questioning Mr. Krabs and SpongeBob for the formula whilst they are stuck inside a mechanical hand. The area where the screw is located can be seen on both sections of the hand, on the right and left hand side. In some shots the right side of the hand completely obscures the screw on the left side, and in some shots not. Also, in one shot, the screw changes colour and becomes white.
Continuity mistake: After Plankton blows up the Krusty Krab roof, Mr. Krabs enters the kitchen through the door leading from his office. When he opens the door, it falls off and leans against the counter beside the door. When SpongeBob approaches Mr. Krabs, the door is suddenly lying on the floor.
Continuity mistake: When Mr. Krabs walks into the kitchen after Plankton detonates the roof, the door falls off and there is no hinge attached to the door, but once Plankton has flown in through the hole in the roof, a hinge has suddenly appeared on the door.
Answer: I believe this is the Season 6 episode "Spongicus".