When you assign an O365 user a Global Administrator role, and this user is assigned a Dynamics CRM license, system will automatically assign a System Administrator role to that user. If later on Global Administrator role is removed, the system will also remove a System Administrator CRM role regardless whether it was automatically or manually assigned.

If you decide to tighten up the O365 security and remove unnecessary Global Administrator rights, find out if any of the affected users have System Administrator role in CRM and whether they need. If they do, you will have to re-assign this role manually.

So if any of your users complain that they can no longer access CRM even though they are administrators, or if you receive a yellow warning that some of the users are missing security privileges, that O365 role clean up could be the reason.