New users added via wpmu_signup_blog($domain, $path, $title, $user_name, $user_email);
are automatically subscribed to the main blog. Can this be prevented? I only want them to be administrators of their newly created blog.
I have no idea where to start looking for that as it seems to be some internal WordPress’s mechanism that handles that.
This is a known bug.
A fix will be available in 3.6.1, see:
http://core.trac.wordpress.org/ticket/25166
For now, either bulk remove the users in WP Admin or do something (ugly and temporary, remove when 3.6.1 is available) like: