There are a couple of ways that you can fix this issue:
1) If you are using Visual Studio 2015, you can go to Tools->Options->Source Control->Environment and change the value of the "Check out folder" dropdown to something other than "Web site".
2) You can also try deleting the temporary ASP.NET files that are generated by Visual Studio. To do this, go to the following folder:
C:\Users\ \AppData\Local\Temp\Microsoft\WebSiteCache
After doing either of the above, you should be able to check in your files without any problems.
