Any <references ... /> tag will apparently consume *all* refs defined up to this point, no matter which group they belong to.
Additionally, different ref links format as discarded and all refs show up as [N], instead of [<group> N] for grouped ones or [<custom>] for specials defined using MediaWiki:Cite_link_label_group-<group>.
Test case: https://pl.wikipedia.org/w/index.php?title=Wikipedysta:Matma_Rex/brudnopis&oldid=32302845&uselang=en (compare HTML and PDF generated via "Download as PDF" in "Print/export" menu).
Version: unspecified
Severity: normal
See Also:
http://web.archive.org/web/20110800000000/http://code.pediapress.com/wiki/ticket/712