This issue is most probably caused by Kentico CMS site has been put into sub-directory of another web site and is inheriting web.config setting from parent folder. If you use same version of 'system.web.extensions' library in parent folder, you can just remove following line from web.config file of Kentico CMS site:
<sectionGroup name="system.web.extensions" type="System.Web.Configuration.SystemWebExtensionsSectionGroup, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35">
Otherwise you can change following lines:
<configSections>
<sectionGroup name="system.web.extensions" type="System.Web.Configuration.SystemWebExtensionsSectionGroup, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35">
to:
<configSections>
<clear/>
<sectionGroup name="system.web.extensions" type="System.Web.Configuration.SystemWebExtensionsSectionGroup, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35">