A WebmasterWorld thread reports that while searching with a site command at Google Search, Google returns results that may be sub domains.
Search Engine Roundtable reports the same:
To be clear, a site command for site:domain.com always brought up sub domains. But I specifically used site:www.domain.com to bring up only results on the main directory. If you have a site that redirects www to non www, or only do site commands with site:domain.com (i.e. without the www) you would not notice much of a difference here).
Further on, Search Engine Roundtable confirms that Google has informed them that this site change is not a deliberate step and the current situation should return back to normal in some time.