Sorry, that was a mistake in the writing of this post. The class tags are present (and the file validates) and it still occurs.
<section epub:type="division">
<h2 class="notes-head">Footnote header</h2>
<ol>
<li class ="notes"><a role="doc-backlink" href="chapter1.xhtml#note1" id="ch1_note_R1">1.</a> Footnote text</li>
<li class="notes"><a role="doc-backlink" href="chapter1.xhtml#note2" id="ch1_note_R2">2.</a> Last footnote text</li>
</ol>
</section>
<section epub:type="division">
<h2 class="notes-head">Following footnote header</h2>
<li class ="notes"><a role="doc-backlink" href="chapter2.xhtml#note1" id="ch2_note_R1">1.</a> Footnote text</li>