When SpongeBob sneaks over from his house to Patrick's in the middle of the night, Squidward's house (usually in between the two) is gone.
When Spongebob's arms are pulled off, Patrick takes Spongebob's right arm off of the box. But when he points at him with it, by the way the fingers are positioned, you can tell that it's a left hand.
When plankton plays one of the notes on the harmonica he walks to the other side of the harmonica and plays the exact same note.