This is a particular problem with 'note' sections, and references used as notes; they commonly include citations for their statements, and you end up with markup that looks like <ref> some text here <ref> a citation for that text</ref></ref>
The VE is for some reason displaying it as a citation template, "some text here", a second citation template and a random </ref> tag. See note 1 in https://en.wikipedia.org/wiki/Fomitiporia_ellipsoidea for example.
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