Back just about a year ago, we covered a change on how webmaster tools handles subdomains. I since forgot about that and now I see John Mueller from Google explaining it again in a Google Webmaster Help thread.
In summary, even though for ranking purposes, Google may not treat a subdomain as part of the internal main domain - Google Webmaster Tools generally does.
John Mueller said in the thread:
In Webmaster Tools we generally treat data from subdomains as being internal with regards to the domain name. With regards to creating a site structure with subdomains or sub-subdomains, we generally leave that to the webmaster :) (though as with other infinite spaces, we discourage the use of wildcard subdomains).
Just a reminder, Google Webmaster Tools and Google's algorithms may treat things different.
Forum discussion at Google Webmaster Help.