Well, first thing to check is to open up the WAR file and see what's inside. You can use 7zip or ZipItFree to open it up since a war file is basically just a zip file with a different extension. Make sure that the web.xml is there and in its proper place.

Also, I use Tomcat myself so I am not familiar with how glassfish explodes its war files. It may be checking the web.xml for validity. Check the web.xml and make sure it is properly formatted xml.