I just killed 4 who were in my shadowshot in the crucible. I did NOT get the shadowshot bounty for killing two or more guardians with a single shadowshot.
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You have to use quiver and kill then with the direct impact from the shadowhot. It is stupid. I played mayhem to finish mine off.
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It is strange that what you did counts as "super kills" for the Vanguard bounty, but it does not seem to count that way for the crucible bounty...use quiver and get the actual kills with the bow for the crucible bounty...
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Try using the Quiver perk for Nightstalker. The bounty says to kill [i]with[/i] Shadowshot, so use Quiver to kill multiple enemies.