I did the upgrade according to.
http://www.asp.net/mvc/tutorials/mvc-5/how-to-upgrade-an-aspnet-mvc-4-and-web-api-project-to-aspnet-mvc-5-and-web-api-2
I solved this problem by reverting the changes that nuget had made to my web.config after running nuget. Revert the changes to a previous working version.