Hi,
There are no limits on a number of roles assigned to a user. I suppose you may have active plugin which can reassign role to a user. Try to grant those role to a user back, deactivate temporally all plugins and login again. Will granted roles will stay as with a user as expected? If Yes, activate plugins back one by one to isolate a reason.
Take into account also that user has a separate role(s) granted at every subsite. So if you granted roles at the main site, but logged-in(switched) to some subsite, user will have their other role(s) granted, until you grant him the same role(s) for this subsite too.
The problem is in the debug there is not a logical reason for deleting the user. And I already made it an network role, so the subsites should also have the specific user role.
WordPress does not support any “network” role. If user assigned to a subsite, user should be granted some role(s) at that subsite. This is done and stored separately for every subsite. Pay attention, even if you added a role to subsite, you have to grant that role to a user at that subsite.