Recently we were helping an academic customer set up their Office 365 subscription for use by staff. The students had been using 365 for some time, and ADFS had been configured for the college's student domain, to enable single sign-on. With the latest version of Azure Active Directory Connect though, there's not much need for ADFS anymore, so we figured it would simply be a case of adding the college's domain name, verifying it, and syncing all the staff username - how wrong we were!
The first error we encountered when trying to import the domain was baffling "Could not verify this domain because it was previously configured for your tenant or for another tenant". Now, being as we were working with the only people who had access to both administrate the subscription and the DNS zone, we were certain it wasn't. Perhaps it was because we had already imported the subdomain and those verification records still existed? We removed them and the error persisted. Removing the subdomain wasn't an option, even temporarily, as it was in use by over 62,000 accounts - to remove an in-use domain requires the username and primary email address is changed first.
So we looked at how the domain could be in use, and there's only one way it can be without DNS verification - Microsoft's self-signup service offered to the academic sector. This allows both staff and students to sign up with a valid school/college/university email address (ending in ac.uk in the UK) and they then have access to Office 365 benefits. Unfortunately, this prevents IT from using that domain with an existing subscription - but there is a way around it that Microsoft have documented here -https://support.office.com/en-us/article/How-to-manage-a-domain-already-in-use-by-people-in-your-organization-who-signed-up-with-their-work-or-school-email-address-b9707ec8-2247-4e25-9bad-f11ddbc686e4?ui=en-US&rs=en-US&ad=US
The issue here is that this can self service sign up can happen without IT knowing - in this case around seven teachers had signed up and had begun using the service. Thankfully there wasn't much data to migrate, but it could have a been a real pain to merge the two subscriptions. I can imagine many institutions transitioned their students away from live@edu into 365 using a student subdomain, and are now at least thinking about moving their staff too, so this could become a common issue.