If you are using Unity.WebAPI package, it depends on System.Web.Http v4.0. In order to use it in Web API v2, you need to add assembly binding redirect to web.config:
<runtime>
<assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
<dependentAssembly>
<assemblyIdentity name="System.Web.Http" publicKeyToken="31bf3856ad364e35" />
<bindingRedirect oldVersion="1.0.0.0-5.0.0.0" newVersion="5.0.0.0" />
</dependentAssembly>
</assemblyBinding>
</runtime>