Hey @BenjaminShorb !
Thank you for posting on the Instructure Community.
At our institution, we've had to do a couple of things when this would occur. A few times we've actually ended up having to delete their user accounts (which for us was okay since they were new accounts and had no grades or other data yet), and we had them re-register on their own with their email and it usually worked. We found that having them sign up is better than an admin creating it for them, at least in our instance.
Another thing we've done is we added on a new login, or we would add on an additional communication method with one of their alternate emails, and they'd confirm that one. Overall, we've done a few different methods, and all have worked for us overtime.
Hope this helps a bit, best of luck to you!
Noah