Relationship disabled by end date but still enabled?
The "Disable expired relationships" scheduled job should set the is_active field to 0 for relationships with a past end date.


  A bit of history: Civi has always treated both past and disabled
  relationships as "inactive" however there were inconsistencies in some
  of the code (reports maybe) that were not doing so. I believe Fuzion
  contributed the scheduled job to remedy this


(From a comment on issue CRM-18561. See also this forum post for some discussion.)

So it looks to me as though the scheduled job has failed in this case. If you view the job log for this job, are any errors shown? Or anything at the relevant time in the CiviCRM log file in files/civicrm/ConfigAndLog/ ?

Could you test whether the problem occurs on the 4.6 demo site?