When utilizing Active Directory and LDAP with users and Built-in Roles, when the Users are removed or changed in the Identity Store and belong to a Built-in role in ArcGIS Server, their respective JSON file becomes orphaned in the configuration store (\..\arcgisserver\config-store\security\user-roles) causing these users to become ‘stuck’ under roles in ArcGIS Server. When this happens, users are not able to be removed from roles. When the deleting process is done, the name is removed, but if the user logs out and then login again, the name reappears. The only way to fix this is to manually delete this file in the configuration store. If JSON files become orphaned in this directory, when a user is deleted from a role, the respective JSON should be deleted from the configuration store.
Go into the respective JSON file in (\..\arcgisserver\config-store\security\user-roles) and delete it so that the user account does not show in the location anymore.