I randomly found the Wormsinger rune, had it in my inventory for some time and then used it. Killed the champion that appeared and then some taken appeared just after, so I killed them too.
Found an Agonarch rune and it said to kill hidden taken threats to charge the rune so I ran around for a bit and found one that spawned, killed the hive major (with Hawkmoon) first and then the acolytes, and it didn't count towards the total.
Went somewhere else in the Dreadnaught and the same thing happened. I killed the hive major first and it still didn't count towards the total even though I killed all the taken enemies.
UPDATE:
Doesn't matter whether you kill the taken with legendary or exotic weapons, it is random as to whether or not you get the kills to count. Killing minions first or killing the hive major first makes no difference.
This quest is bugged and needs to be fixed.
UPDATE 2:
Stuck at 2/7, running around and killing taken but nothing is working.
[u]UPDATE 3[/u]:
I know what I'm doing now, it's not a bug so Bungie and players can disregard this post.
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You said hive for the first two then said taken so I think you have it at least figured out
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The Agonarch rune has a daily target. These targets are those majors or yellow bar taken enemies that spawn in after you activate those taken circles in the breach and mausoleum area of the dreadnaught. Currently there is a way to charge your rune off of a fully charged rune. It's all about patience and making sure you defeat the daily target.
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You can only kill one per day.
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After 1st drop it was ok -ive done all bosses and chest quest. 2nd Argonach rune is broken for me - 0/7. No matter how many taken majors i kill its still null.
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Hey man, just so you know, you can transfer the rune to your other characters and kill the hidden threats on them and you can charge it 3 times a day. Hope this helps.