Forget about the Zoras and the ragno House, there's a MissingNo in Great Bay!

Could someone tell me why my game removed all my data of Great Bay? I had gotten the map and compass, as well as the Ice arrows. I saved once. Then returned to the dungeon. I died against the frog-ish thingy, I was then back in Clock Town. Without the Ice arrows, the song (New Wave Bossa Nova) even the map showed that I hadn't visited Great Bay! But somehow, I had the bottle and Zora Mask...can someone tell me how this happened?