Is there a way around this? I've also run into this issue and have done everything else aside from the last couple of fairies and the secret corridor.
As for why this glitch happens, is it possible that the Wind Fish warp happened one after the other, causing one to glitch?
Is there a way around what? I'm not sure which of the matters discussed you're asking about.
The two warps are separate, scripted events and not related to the way that screen secrets normally work.
So, the way it happens is during the first Wind Fish event; the script changes the combo for the door to the Trendy Shop to a different combo.
As a result, you can now find Farore inside.
This also changes combos inside the Dream Shrine so that when you return there you are warped to a different event.
Then, the second Wind Fish event triggers a change inside the Trendy Shop which will warp you to a duplicate room when you enter.
That room has yet another script which looks for the Wrapped Present and if it is in your inventory; warps you to the end of the Trading Sequence cutscene.
Theoretically, you could use cheats to warp to the right place if you knew where that was.