From the Microsoft article here, ASP.NET 4 Child Applications Fail to Start When Under ASP.NET 2.0 or ASP.NET 3.5 Applications. You'll need to put inheritInChildApplications="false" into your parent ASP.NET web.config file.
Here's the example they show in the article:
<location path="" inheritInChildApplications="false" >
<appSettings />
<connectionStrings />
<system.web>
<!-- Removed for brevity -->
</system.web>
<system.codedom>
<!-- Removed for brevity -->
</system.codedom>
<system.webServer>
<!-- Removed for brevity -->
</system.webServer>
</location>