Just about every book, TV show, movie, video game/video game series with a plot etc. have something that doesn't make sense and SpongeBob is no exception. So discuss them here!
The most obvious is what happened at the end of the movie, but lots of episodes have it too. I know it's only a cartoon, but sometimes it's fun thinking up theories. Here's my example:
I Was A Teenage Gary: The ending.
My theory: My theory is that this episode was when Sandy was a scientist, and she found the snails there. She didn't realise at first, but eventually she saw they had similarities to Squidward and SpongeBob, and eventually realised it was them, and changed them back.