Late last week, Google released a new feature for Google Webmaster Tools named Site Health. Google is pushing the main issues of your sites right on the home page.
The issue is, the site health tool is not perfect, it has health problems of its own.
A Google Webmaster Help thread reports Google listing two of the same site, one with the main domain and one with the Google Webmaster Tools URL. Yea one says, www.carhireflorida.net and the other says https://www.google.com/webmasters/tools/dashboard?hl=en&siteUrl=http://www.carhireflorida.net/.
Weird? Yea, for sure. Here is a screen shot:
Pierre Far from Google responded saying:
Thanks for the report. I've passed on the screenshot to the relevant team internally.
Also, Webmaster Tools does not affect ranking like this. They're separate things and Webmaster Tools is merely a reporting interface for how Google sees your site.
Forum discussion at Google Webmaster Help.