The monthly refreshLinks.php --dfn-only cron jobs do not seem to be running. A straightforward SQL query returns rows that should have been deleted, and a check of the deletion logs for those page IDs suggests that this has been the case since at least August 2014.
Perhaps someone could check /var/log/mediawiki/refreshLinks/s2@2.log on terbium, or some other relevant log file, for an indication of an error?
On that particular wiki, all the pages were in the File namespace, which suggests that there may be a bug in MediaWiki. That, however, would be a separate bug from any that might be affecting the cron jobs.