A referenced node is missing--when did it disappear?
Drupal 7 does not delete references to deleted nodes by default. See the Field reference delete module. Some details about it, from its project page (check that page for even more details):


  This module removes references to a deleted entity from fields stored in an SQL database. It exists to prevent stale references to non-existent content from causing unexpected problems (for example, when the referencing content is being displayed).


I'm not sure if it will clean up existing "dead" references, but at least moving forward it does.