If this is still an issue you're facing, have you checked the sitemap settings to see which page types are getting included? For example, a site with a few thousand tags that are not entered in the sitemap but not yet set to noindex could easily produce extra pages like this.
The next step is parameterization. Anything going on there with search URLs or product URLs? eg ?refid=1235134&q=search+term or ?prod=152134&variant=blue
If you really want to scrape through Google, get a list of your sitemap and scrape queries like "inurl:domain.com/a", "inurl:domain.com/b", "inurl:domain.com/c". etc. This should allow you to dive deeper into the site map to see what Google really has indexed. For URL subfolders with tons of URLs like domain.com/product/a, you'll want to do the same thing at a subfolder level instead of root URLs.