Hey,
Last week a change to ignore empty references in lists of references was made: https://github.com/wmde/WikibaseDataModel/pull/399
This means that no new empty references can be added, and that existing ones will no longer be visible in most places. The one exception I can think of are dumps, since they use JSON generated before the change was made. Making a single edit to an entity that has an empty reference will fix it there as well though.
Note that this change has not yet been deployed to Wikidata.org.
Cheers
-- Jeroen De Dauw - http://www.bn2vs.com Software craftsmanship advocate Developer at Wikimedia Germany ~=[,,_,,]:3