Did that really happen? Like existing and populated with existing files /user/Documents content had been moved automatically to the /user/OneDrive/ without asking? No offense, but I have a hard time believing it.

If if was a new setup and people accidentally started using OneDrive dir as a primary folder and then something broke, then yeah, that may happen. Or if the users got conned into enabling automatic backups for folders. That's also possible. The problem is that backup setting is off by default. But automatically copying or moving files from outside of the /user/OneDrive without any prompting?