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From https://bugzilla.wikimedia.org/show_bug.cgi?id=50749#c2

Look at [[Otto I]].  It has 63 references, including ref #18 ("Thompson") from explanatory footnote [d].  This ref doesn't appear in VisualEditor.

http://en.wikipedia.org/wiki/Otto_I%2C_Holy_Roman_Emperor?oldid=621934593
http://parsoid.wmflabs.org/enwiki/Otto_I%2C_Holy_Roman_Emperor?oldid=621934593

This broke in https://gerrit.wikimedia.org/r/#/c/143362/

Change 155661 had a related patch set uploaded by Subramanya Sastry:
(Bug 69827): Supported nested <ref> tags once more

https://gerrit.wikimedia.org/r/155661

Change 155661 merged by jenkins-bot:
(Bug 69827): Supported nested <ref> tags once more

https://gerrit.wikimedia.org/r/155661

Now deployed. Please reopen if necessary.