kfallconnect, if the 404 errors are being picked up as duplicate content, then most likely they're not actually showing up as 404 error pages. It's quite possible that it's a 404 error on the site (that's what the user sees) but, in fact, the server header is not displaying a 404 error. It could be showing up as a "200 OK".
First, I would identify the pages. If the user sees an error on the page, then that's fine. Use a server header check tool to see what the response code is when someone goes to the page. You can use something like Rex Swain's HTTP header tool to check it: http://www.rexswain.com/httpview.html . If the page shows a 404 error then you should be fine, it's not duplicate content.
If the page is showing a "200 OK" then it most likely IS duplicate content. If the page is showing an error to users but showing a '200 OK' in the server header, then that needs to be fixed.
But if the page is showing actual content (and not an error to visitors) then you need to look at potentially using the canonical tag or removing the content on the site completely (which is preferred).