http://en.wikipedia.org/w/api.php?action=query&list=exturlusage&euquery=www.cia.gov/cia/publications/factbook/geos&eunamespace=10&euprotocol=https does not show all links as expected. e.g. http://en.wikipedia.org/w/api.php?action=query&prop=extlinks&titles=Template:Economy_of_Austria_table contains that a link that should match.
I think its because ApiQueryExtLinksUsage uses el_index to find these links. But as i can see on toolserverdb, in the missing cases el_index on db externallinks is empty. I think el_to should be used in the query instead.

sql query to show the missing result on enwiki_p: select page_namespace, page_title, e.* from page p inner join externallinks e on p.page_id = e.el_from where el_to like 'https://www.cia.gov/cia/publications/factbook/geos%' and page_namespace=10;

Version: unspecified
Severity: major
URL: http://en.wikipedia.org/w/api.php?action=query&list=exturlusage&euquery=www.cia.gov/cia/publications/factbook/geos&eunamespace=10&euprotocol=https