rc.php_ini_setup should filter out duplicate extensions.ini values as is done during an upgrade
In some rare edge cases (e.g. corrupted pkg db, forced pkg reinstall) duplicate entries can end up in /usr/local/etc/php/extensions.ini. These are cleaned up on upgrade but it also makes sense to do so during the php.ini setup process to avoid errors at other non-upgrade times.
I have a fix pending, ticket is for tracking purposes.