No, it isnt that much serious, because usually /pages/index.php doesnt appear anywhere. It exists, but there is no link to this page.
And concerning "Duplicate Content" - there are lot of horror stories about it, the simple truth about it is: If there are 2 pages with the same content on the same site, Google lists the one which is more important.
But with less weight. = lower listing in the search engineer.
And if you link to the login page, and you ain't logged in you are redirected to /pages/index.php thats kind of a link?
