Cite emits false duplicate errors when using {{#tag:ref}} with XML-style tags inside. For example:
{{#tag:ref|<nowiki>foo</nowiki>|name=foo}}
{{#tag:ref|<nowiki>foo</nowiki>|name=foo}}
<references />This is because, due to using #tag, the Cite extension doesn't look at the original wikitext as written above, but only after the XML-style tags have been replaced by strip markers.
While the example above is better written as the following, which doesn't cause the issue:
<ref name=foo><nowiki>foo</nowiki></ref> <ref name=foo><nowiki>foo</nowiki></ref> <references />
…this problem is impossible to avoid when nesting <ref> tags (which is bad but people do it anyway, often without realizing it due to templates like {{sfn}}), which is only possible with {{#tag}}:
<ref name="Buna">Advance to Buna</ref>
{{#tag:ref|Buna<ref name=Buna />|name=Blakeley}}
{{#tag:ref|Buna<ref name=Buna />|name=Blakeley}}
<references />