I think this is a bug because I’m seeing the same thing on my subfolder setup after upgrading.
URLs work fine if you visit them directly, and the links in the markup are correct, but when JS takes over for navigating between pages it omits the subfolder path from the URL when it calls history.pushState().
So while the navigation works the URL presented to the user is wrong, which is a bit of a problem because if someone copies the link to share it it’s going to 404.