This one can eaily be fixed. In
display_format_helper.php, all your spans are given ids, but these result in invalid HTML since all IDs on a page have to be unique. You should rather use classes. If your script needs the IDs for some reason, you should autoincrement them or something to make them unique.
Some example output:
<div class="reference journal_article"> <span id="authors">Albertus, Y, R Tucker, A St Clair Gibson, E Lambert, D Hampson, and T Noakes</span>. <span id="publish_year">2005</span>. <span id="title">“Effect of distance feedback on pacing strategy and perceived exertion during cycling.”</span> <span id="publication_title">Medicine and Science in Sports and Exercise</span>, <span id="volume">37</span> <span id="issue">(3)</span>: <span id="pages">461-468</span>. </div>