Web.config files inherit from their parents, so if your root website is setup for MVC your application web.configs will inherit those settings.
In this case the root web.config likely added a couple of assembly references which you will need to strip out. The easy way is to add a <clear />
rule to the assembly section (in system.web):
<compilation>
<assemblies>
<clear />
<!-- add new assembly references here -->
</assemblies>
</compilation>
The alternative is to use remove
rules which alllow you to remove specific references.
<compilation>
<assemblies>
<remove assembly="System.Web.Mvc, Version=2.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
</assemblies>
</compilation>