The cracked wall near the entrance of the wind shrine respawns every time you exit the shrine, and so do the 30 coins behind it. This makes it ridiculously easy to get the shield, p ring, and beam gem.

When the flail knight dies, the spiky balls can sometimes get stuck in doorways.

Some of the dirt tiles in the overworld don't seem to be there for any reason. They're not blocking anything.

There's a door in the bottom-right part of the fire shrine that doesn't have a keyhole, and can't be opened even by the master key. I couldn't find a lever either.