You are absolutely right. But if you think that you have duplicate content issues, then Screaming Frog can help you tease that out.
That is also why I suggested the SEOmoz tool, since it is supposed to mimick a SE spider, it can give you a pretty good idea of any issues that you might have.
Using the advanced operator of site:domain makes sense, but if there are issues there like eyepaq said, it is going to be tough sledding.
My suggestion would be to download take a closer look at what GWT is telling you. Are there duplicates there? Is your CMS auto-generating URL's? That is probably going to be your best bet IMO.
Best of luck!