Google See’s your domain. say www.bettermychance.org and www.bettermychance.org/index.php as two different pages with the same content on both. so a great way to solve this problem is by putting some code in your .htaccess file

Here is what you do:

Options +FollowSymLinks
RewriteEngine on
RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /index\.php\ HTTP/
RewriteRule ^index\.php$ http://www.bettermychance.org/ [R=301,L]

Replacing my domain above for yours.

Now when anyone goes to your domain.com/index.php they will be redirected to your main URL thus eliminating the chance of a duplicate content penalty.