Not all kills on Wizards/Knights count towards "The Extermination" Quest Start from Eris. It does NOT say that they need to be Majors and/or Ultras so either way, something needs to be fixed.
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They don't. I did this bounty with the traveller shard being poisoned by the three witches mission. You will meet plenty of normal Knights and wizards on the way and they count towards the bounty.