Here's one scenario I've run across and it could be happening to you!
Does your site have a home-brew search page, where you query your own local database and display the results?
Did you have that search page blocked in robots.txt and set to meta NOINDEX?
No?
Got AdSense and Google Analytics on those search results pages?
Bummer dude.
I recently stumbled across tens of thousands of duplicate pages in Google, maybe hundreds of thousands, pages that should have never been there logically because they didn't exist. You have to submit a query into a form, POST it, and then get a list of results, there are no links to this content from the website or the outside world, yet it exists in the index.
Apparently thanks to use of either AdSense of Analytics, maybe both, Google also saw every page of search results and indexed that crap and just kept indexing it until it overflowed into a mind blowing number of pages that nobody would ever know they had indexed because they obviously don't generate any traffic.
If you have a custom search, I'd suggest you go look to see if the results of those searches are being indexed ASAP because it could be all that stands between you and a thing content penalty.
Regardless, block your site search pages with robots.txt and meta NOINDEX just to make sure Google's other tools don't feed Googlebot any data it shouldn't have.
Live and learn.