My first guess is that Tidy is the culprit. Try the input

<ref>foo</ref><ref><div>bar</div></ref><ref><table><tr><td>baz</td></tr></table></ref>
<references />

on Wikipedia.
The first reference is correctly wrapped in a <span class="reference-text">, in the second reference this span is moved inside the <div>, in the third it is missing completely.

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