During your first encounter with Kaepora Gaebora, there's a window of time where you can enter an action input (e.g. swinging the sword, using the C buttons). If you do so, something breaks and the camera doesn't stay on Kaepora Gaebora when he flies away and instead returns to Link. At this point, no controller or keyboard input works and Link is unable to move. If you make sure to only hit the A button during this interaction, you can avoid the issue.

I'm running on Windows 10 version 19043.1586 using the D3D11 backend.

Here's the save file I can reproduce this with:
oot_save.zip