How to reproduce:
1) Play normally through to rescuing Ku and the confrontation with Shriek.
2) Proceed back to Silent Woods for the hide-and-seek with Shriek sequence.
3) Use the save well directly after escaping Shriek.
4) Proceed through the wastes to the Burrow spirit tree and activate it.
5) Congratulations, you are now trapped.

It is impossible to use Burrow, even though you got it. Even though on screen tooltips tell you to use it.

The softlock gets weirder!!

6) Access Backup Saves
7) Load the most recent Silent Woods save
8) You will spawn at the Burrow tree, riding on Ku!
9) Congratulations, you are STILL TRAPPED!