First off, I'm so sorry this is happening.
My hypothesis here (which you seem to at leas suspect) is that some how it got confused about which tenant/organization they were trying to sign up for. It's possible this happened because nobody touched the browser for the session timeout period (which I thought defaulted to 60 minutes but it may be set to 20 minutes) and then when they went to submit the form it didn't know what tenant they were trying to use anymore so it "guessed" the master tenant or another tenant. Of course, I'm assuming that it was sitting around long enough for the session to time out. Hitting "reload" or reloading your URL right before having someone register might mitigate that if it's what's happening.
I suspect what has happened is that those patrons are registered in a separate tenant/organization and somehow they were able to associate with family members who are in your tenant/organization. This shouldn't have been allowed to happen, if that's the case. If that's what happened it would be a code problem and it would be on me.
When they log in, they are seeing your program? Or possibly another tenant/organization?
To answer your issues:
There's a single patron database table that all patrons are in (this is why people across tenants cannot use the same username currently). If they exist then they're in that table. All I can figure is that they're set with the wrong tenant.
I'd need to know a little more to fully understand how to bring these people back into the fold (so to speak). My guess here is that the software doesn't have the capability to do that as-is but we know these people exist in the database so one way or another we can get them in the right place (either a database query or adding a feature to the Control Room).
If my hypothesis above is correct the fix for the symptom is to have them click that link just prior to registering to ensure their session hasn't expired. I had thought that this problem was fixed in the work I did earlier on multi-tenancy (i.e. if the session is timed out it should redirect patrons to the
Select.aspx document of the master tenant).
I could tell a bit more if I had access to your database or a backup of it. I'm not sure the comfort level providing me with either of those but it would help diagnose what's going on. Also, as usual, any log files on the disk could help.