We usually use User Group Memberships to administer user's permissions. I discovered that when a User Group was removed from User Group Membership, the permission sets of 'System' scope remained at the User Permission Sets table. This happens to existing users of environments that went through upgrades/updates. I tested the same scenario in all upgraded environments and the same problem occurred. I reported the issue to Microsoft support but I was referred to submit an idea here. Please help vote to get this issue resolved.