There was a bug with documents with more than one anonymous footnotes, which would all end up to reference the first one only. The patch fixes this problem.
@@ -286,6 +286,7 @@ referenced sequence."
(setq def (match-string 4)
ref (or (match-string 1) (match-string 2))
before (char-to-string (char-after (match-beginning 0))))
+ (if (equal ref "fn:") (setq ref nil))
(if (and ref (setq a (assoc ref ref-table)))
(setq marker (nth 1 a))
(setq marker (number-to-string (incf count))))