WordPress Multi-Site shares it's user database. So if they have already registered on one site, they can't register on another site.
Multi-Site user management is complicated and not very user friendly. They may exist as a user in the user database because they registered on another site, but won't have access to that site.
Currently the User Registration Add-On only creates new users, since this user already exists in the user database there is nothing it can do.
This is one of the downsides to using Multi-Site to manage sites that you want to enable individual user registration on. It's one of the reasons individual WordPress sites may be easier to manage because Multi-Site and available plugin solutions do not make it easy because of how the data is stored.
Another solution is to look at other plugins that manage user access in multi-site such as:
Posted 8 years ago on Thursday June 23, 2011 | Permalink