This happened on PC but may be on all versions.

I took the Animal Friend perk. Actually I took two levels of it this game.

I knew the Legion Mongrel would not fight the Legion Faction for me.

I should not have had to kill the last breathing survivor at the Cove, the Legion Mongrel, for the Eye For An Eye quest to update and see it as all Legionairy were dead. The Legion Mongrel should be exempt when you have the Animal Friend perk. As soon as the dog was dead, the quest updated.