After updating to VS 2015 update 1, if I run a web project (MVC), stop the application, then try to run it again, VS stops and pops up a dialog claiming
Check that the IIS Project URL actually points where you think it does. If in doubt, click the 'Create Virtual Directory' button.
I had this issue recently where I had been running a temporary version of a production codebase and had repointed the folder in IIS to the temporary version, which was, indeed, running a production build, not the debug version I was trying to debug.