Ah ha! So glad I found this thread, I at least know I'm not crazy. I'm having the same issue with using the multisite user management plugin. This is the culprit, right?
So what do I need to do to prevent this from happening? Stop using the plugin, and find an alternative? Or, do I need to deal with spam users in a different way?
I guess I don't quite follow why marking certain users as spam, marks affiliated sites on the network as spam too...