The Container Adaptor implementation should handle this. If you're having problems you can try to debug the relevant code here:
One possible reason on top of my head is that you are attempting to deploy a Servlet 2.5 app on Tomcat 7. This triggers a 'bug' in the Arquillian Servlet Protocol. Basically since Tomcat 7 is set up with the Default protocol Servlet 3.0 it will use web-fragments. But Tomcat 7 in Servlet 2.5 mode won't understand that.
A possible workaround is to force the use of Servlet 2.5 protocol on those deployments by using @Deployment @OverProtocol("Servlet 2.5")
Thank you Aslak,
That fixed it.