You can add the <location> element with the “inheritInChildApplications” attribute to the root web.config. This attribute will prevent child applications inherit some specified configuration from the root web.config.

The attribute must be placed in the <configuration> section of the web.config. It looks like this:
<location path="." inheritInChildApplications="false">
<system.web>
 <!--
     ……
     Your settings

  -->
</system.web >
</location>

Referance:

SectionInformation.InheritInChildApplications Property