I have been creating test users for all my wordpress multisites that I have been standing up. There is one users that I can not remove. He is set as an administrator on one site I have but not the main one. What I have been doing is changing the roll to something low. Remove him from the site. That will remove him, then when I go into the Network site and go to users to completely remove the user it will reset that user back to what it was before. It will put him back in on the site and set him to an administrator.