Depending on your case, there are three possible scenarios:
see this link http://www.beansoftware.com/ASP.NET-FAQ/Directory-App_Code-Not-Allowed.aspx
Basically, If you precompiled your app, there shoudn’t be an App_Code folder. If you added it later, you should delete it.
OR
May be Somehow a precompiled.config file has made it to production. Deleting that file should resolve the App_Code directory error.