Emulator

The name ID didnt show up. Its The Legend of Zelda Skyward Sword "SOUE01"

Try disabling the dual core option and then report back: if the game doesn't freeze anymore maybe this could be a FIFO problem.

luc: Are you using savestates at all?

hatarumo: If this is happening randomly, it's going to be tough to find out if disabling dual-core fixes this or not. The game may just happen to not crash at the time he tests.

I'll try to disable dual core option, and i'll report back as soon as i can.
For the save state, yes i use them, but the problem started before that. I started to use save states frequently just to avoid having to return too much on the game because of the freezes

Savestates can cause issues like this, I'd suggest starting the game over with only using the in-game saves and see if this still persists. That may not be something you're willing to do depending on how far into the game you are, but since the game is not acting right anyway, it's worth the effort for you to be able to play through the game properly. If you don't, we'll never know if savestates is indeed the cause.

for me is this problem in Dolphin v3.0-776 too, the LLE plugin fixed the bug a little bit, in version 3.0-631 is this problem not and worked with the HLE plugin too.

Post a game save to the area in question.

Here is a the Save. Sorry about the long time i took to answer, i was in a business trip abroad.

I tried without dual core mode, and it still freezes. This save is in the area that it keeps freezing.

Also i can confirm that LLE fixed the problem, but my computer isn't powerfull enough to run it in LLE mode.

I can also confirm that it works just fine in Dolphin v3.0-413

Forgot to mention that in this save, it is the third file!

I cannot find a "door" or "passage" within a 7 mile radius of your save file 3's starting location..
Please explain how to reproduce the issue.

I haven't seen this issue even once so far, and I've played through a pretty good portion of the game (at the desert now).

Was this fixed with the new-ax-hle merge possibly? If someone reminds me of which master commit that got merged into, I might mess around with the revisions around it and see if it's fixed.