By default, ASP.NET applications setup in sub directories will inherit from any web.config file that exists in the root web site folder.
This can cause conflicts as the sub application will attempt to load any assemblies referenced in the root web.config from the sub application's own bin directory, causing a file not found error.
To prevent the sub application from inheriting the root web.config, the root web.config <system.web> section can be wrapped with a location tag as follows:
<location path="." inheritInChildApplications="false">