Hope Nintendo will patch this is the next update

This GameFAQs thread doesn't really shed any light on it, but I'd naïvely guess (take it with a grain of salt) that you're brushing up against the sprite limit.

This was a lucky happenstance. Even happened occasionally on the cart. It's a harmless (literally) overflow error. It's kind-of a sprite error. The game is divided into actual "screens" and you just scroll smoothly through them. If the game UNLOADS to many sprites from one you just left, the buffer fills up and it can't load in new ones as there's no way to dispose of them (going through doors usually does this). That's why it "fixes itself" occasionally. This also sometimes causes these seahorse things to just plain not generate, but they are still actually there, and can hurt you.