Host Asp.Net Web API as an Application Under Asp.Net MVC application on IIS

This was resolved by setting inheritInChildApplications=”false” on the web.config file of the Asp.net MVC Application.

  <location path="." inheritInChildApplications="false">
    <system.web></system.web>
  </location>

  <location path="." inheritInChildApplications="false">
    <system.webServer></system.webServer>
  </location>