<compilation debug="true">
   <codeSubDirectories>
 <add directoryName="VBCode" ></add>
        <add directoryName="CSCode" ></add>
   </codeSubDirectories>
</compilation>

Here VBCode and CSCode could be your directories withinn the App_Code folder for .vb and .cs files.
We have to put the language spacific code files in specific folder for the successful compilation.

Otherwise following error will occur:-

The files '/App_Code/Class1.cs' and '/App_Code/Class2.vb' use a different language, which is not allowed since they need to be compiled together.