I am curious, when someone comments it creates a link to the bottom of the content that was commented on How is this not seen by search engines as a link on the same domain to the same content in other words, why is it not considered duplicate content it is a slightly different URL with the same content.
The url is only different after the #. The search engines ignore anything after a # in a url. The search engines know that index.php is the same as index.php#footer. The info after the # is just a anchor to a specific place on that page.