Both a-tags have identical hrefs, both li-tags have identical about attrs and ids whereas they shouldn't since the hrefs point to different references and ids should be unique on a page.
[subbu@earth lib] echo "X <ref>one</ref> <references />\n\nY <ref>two</ref> <references />" | node parse
<body data-parsoid='{"dsr":[0,65,0,0]}'>X <span about="#mwt3" class="reference" data-mw='{"name":"ref","body":{"html":"one"},"attrs":{}}' id="cite_ref-1-0" rel="dc:references" typeof="mw:Extension/ref" data-parsoid='{"src":"<ref>one</ref>","dsr":[2,16,5,6]}'><a href="#cite_note-1">[1]</a></span> <ol class="references" typeof="mw:Extension/references" about="#mwt4" data-parsoid='{"src":"<references />","dsr":[17,31,2,2]}' data-mw='{"name":"references","attrs":{}}'><li about="#cite_note-1" id="cite_note-1" data-parsoid="{}"><span rel="mw:referencedBy"><a href="#cite_ref-1-0">↑</a></span> one</li></ol>
Y <span about="#mwt7" class="reference" data-mw='{"name":"ref","body":{"html":"two"},"attrs":{}}' id="cite_ref-1-0" rel="dc:references" typeof="mw:Extension/ref" data-parsoid='{"src":"<ref>two</ref>","dsr":[35,49,5,6]}'><a href="#cite_note-1">[1]</a></span> <ol class="references" typeof="mw:Extension/references" about="#mwt8" data-parsoid='{"src":"<references />","dsr":[50,64,2,2]}' data-mw='{"name":"references","attrs":{}}'><li about="#cite_note-1" id="cite_note-1" data-parsoid="{}"><span rel="mw:referencedBy"><a href="#cite_ref-1-0">↑</a></span> two</li></ol>
</body>
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