The file web.xml in the deployment unit is going to modified at deployment time.
The old file is renamed and a new modified one is created to bring web.xml in sync with webservices.
If the two files already fit the app will also work although the renaming nd replacing of web.xml fails, like in your case.
The cause for the rename problem itself is a missing right on the file web.xml for the user running the jboss instance.
I saw this, when I deployed a web-app as a war directory structure instead of putting it all together in one war-file.