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:
Just a reminder, Google Webmaster Tools and Google’s algorithms may treat things different.
Forum discussion at Google Webmaster Help.
