The Google Webmaster Central Blog has a post on common questions sent to them about data issues found in Google Webmaster Tools. The short answer that Google gives is that if the data is off, then it might be due to your site being listed in Google as both the www and non-www and also subdomains being listed as unique domains.
Google may consider www.example.com different than example.com. You may own example.com and example.org and Google will consider those individually. You may want Google to group subdomain.example.com with example.com and they may not being doing so.
Google offers tips on how to get the most out of your reports:
- If you feel like you’re missing some data, add both the www and the non-www version of your domain to your Webmaster Tools account. Take a look at the data for both sites.
- Do a site: search for your domain without the www (e.g. [site:example.com]). This should return pages from your domain and any of your indexed subdomains (www.example.com, rollergirl.example.com, etc.). You should be able to tell from the results whether your site is mainly indexed with or without the www subdomain. The version that’s indexed is likely to be the version that shows the most data in your Webmaster Tools account.
- Tell us whether you prefer for your site to be indexed with or without the www by setting your preferred domain.
- Let everyone else know which version you prefer by doing a site-wide 301 redirect.
Still have issues, join the Google Webmaster Help Group and hopefully a Googler can help you with your specific issue.