Our site has a 404 Page that is served when an invalid URL is entered into the browser:

e.g. http://www.bevnet.com/Aisle-Grocery/b/ref=sv_gro_0?ie=UTF8&node=52128011

Unfortunately, it seems the Sitemap Generator considers this a real URL, and adds these bad URLs to the sitemap. Is there a way of filtering these out?

If the website does not return a 404, the software cannot determine it's a 404.
One thing you can do is let the software spider the entire site, then edit the results, sort by title, and delete all that have the 404 title.