I know that when I selected my site to always be WWW. version, G asked me to verify the non-WWW version by entering it as a second site - which is exactly what you have now.
It sounds like it happened "by itself" in your case, and that is new for me.
In regards of the two site versions, actually www and non-www can be different sites.
It seems to be an assumption that those would be the same site. As you may have noticed, there are instances like ww2, ww3, or www3, not even sure now... and all of these could be different sites as www is simply a subdomain of the main domain.