This might happen if you place .cs files in App_Code and changed their build action to compile in a Web Application Project.
Either have the build action for the .cs files in App_Code as Content or change the name of App_Code to something else. I changed the name since intellisense won't fix .cs files marked as content.
More info at http://vishaljoshi.blogspot.se/2009/07/appcode-folder-doesnt-work-with-web.html