I've been using Sitemaps for years now, but recently I have come across an issue I've not seen before. The site in question is generated by a database using php. all URL's are rewriten using the RewriteEngine in htaccess. So 'domain.co.uk/category.php&cat=3' becomes 'domain.co.uk/description/index.php'. So in my sitemap.xml file I have 'domain.co.uk/description/index.php' however Webmaster tools flags 'domain.co.uk/description/' (without the index.php) as "404 (Not found)" Firstly I have no links at all pointing to 'domain.co.uk/description/' they all point to 'domain.co.uk/description/index.php' and secondly it's saying that the URL is listed in my sitemap file when it is not? I suppose that I could look at rewriting requests for 'domain.co.uk/description/' to 'domain.co.uk/description/index.php'. Any advice?
It seems that you are rewriting the dynamic URL to static URL which doesn't exist and that's the reason it gives you 404 error. I would advice you to keep dynamic URL in your site map which will redirected to static URL.
I would suggest you to keep only direct urls in your sitemap as redirected urls may show you some sitemap problems..