Your website can be accessed with www.domain.com and domain.com. Since Google penalizes this due to duplicated content reasons, you have to stick your domain to either www.domain.com or domain.com. You can fix this easily with .htaccess:
Ex: to redirect all traffic from http://domain.com to http://www.domain.com
RewriteEngine on RewriteCond %{HTTP_HOST} !^www\.domain\.com RewriteRule (.*) http://www.domain.com/$1 [R=301,L]
To redirect http://www.domain.com/index.php to http://www.domain.com
RewriteEngine on Options +FollowSymLinks RewriteCond %{THE_REQUEST} ^.*/index\.php RewriteRule ^(.*)index.php$ http://www.domain.com/$1 [R=301,L]
Option 2:
RewriteCond %{HTTP_HOST} ^www.domain.com RewriteRule (.*) http://domain.com/$1 [R=301,L] RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /index\.php\ HTTP/ RewriteRule ^index\.php$ http://domain.com/ [R=301,L]web