Emulator

And I'm running dolphin 3.5

Sorry most of my interest was to help the project. I wasn't sure if it was just me experiencing this issue

This keeps happening to me and this is the first place I have someone else who has encountered this issue. Did you figure out how to fix it?

Yeah, I was messing around with AR codes before that happened. So I replayed the game without cheats. And it didn't do it. I think it's because right on the start of the game I swam to Forest Haven with "sprint with A" cheat. And supposedly the King of Red Lions is talking to you, I think that's the glitch when he asks you constantly about the sail

I used super hookshot to skip everything after the telescope and I think that's my problem but are there any known fixes?

Not really except starting the game over again.