Apache shouldn't be logging any included PHP files unless you're including them using the virtual() command or you're including them using the full include( "http://..." ) path.
Either of those two methods actually make a call back to the web server to load the include.
Using an include() command without the full URL specification, without the "http://", will cause Apache to load the include from within the current page view, only logging one hit to the web server logs...
Check your include statements to see what syntax they're using.
