IIS website with Web Application

Hi 

I have developed and deployed .NET Framework 4.0 based Web Services to IIS which is working fine.

Now I want to deploy the MVC based REST API to the same Site as an Application which also i have done it using Web Deploy Package. When I hit my REST Url it give me an error of Access Origin for that i have also applied the corresponding changed in Web.config file. (in both the Web.config)

If i deploy the same REST Services in separate site. it just works fine.

Does any one have any suggestion on the same?

Thanks, Parth