This is the scenerio - You have a main site, you add a blog at /blog and a forum at /forum. When you run the /blog or /forum you get errors that it's looking for a DLL used by the main site. You wonder why /blog or /forum would need a specific assebly used by main site. The answer is the nested asp.net apps "inherits" web.config from the main site.

How do you prevent it? Here, add <location tag as follows to the web.config of the main site

<configuration>
    <configSections>
        ...
    </configSections>
    <location path="." inheritInChildApplications ="false">
        ... rest of config
    </location>
</configuration>