consider 
<?php foreach($certificates_list as $certificate): ?>
<div class="certificates_list">
    <p><?php echo link_to($certificate->getName(), "certficate", 
            array(
            "id" => $certificate->getId(), 
            "name" => $certificate->getNameSlug()
            ));
            ?></p>
</div>
<?php endforeach; ?>

1. select everything that is in foreach body and format - works fine 
2. select everything from <p> to </p> and format. I invoked formatting twice and ended up with

<?php foreach($certificates_list as $certificate): ?>
<div class="certificates_list">
    <p><?php echo link_to($certificate->getName(), "certficate", 
                                            array(
                                            "id" => $certificate->getId(), 
                                            "name" => $certificate->getNameSlug()
                                            ));
                                            ?></p>
</div>
<?php endforeach; ?>