Canonical HTML (from PHP parser):
<sup id="cite_ref-Forty_47-0" class="reference"> <a href="#cite_note-Forty-47"><span>[</span>47<span>]</span></a> </sup>
Output from Parsoid:
<span id="cite_ref-Forty-46-0" class="reference" about="#mwt408" typeof="mw:Object/Ext/Cite" data-parsoid="…"> <a href="#cite_note-Forty-46">[47]</a> </span>
I have no idea if the inner spans have any value, but the outer span should be a sup element instead.
(Also, the names of the cites are indexed from 0 in names but 1 in label - 46 vs. 47, whereas in PHP parser they're indexed from 1 in both; not sure if this is a problem.)