If the button isn't showing up, that's usually not due to a misconfiguration in the backend. It's usually because the Javascript library isn't loading properly, which can be caused by trying to use multiple Facebook components on your site or by using a Share button (which has conflicts with Facebook's own libraries).
As for the misconfiguration, if your site is
www.domain.com, then disregard the warning. We try to make it 'smart' to diagnose most common issues, but it's not foolproof. Basically, just check your site URL and Domain URL's in the Facebook application, if they're correct, you're good to go.
Hope this helps!