During the final boss encounter of the warden of nothing GM, none of the champions spawned in and the boss immediately entered the field when we touched the arena. After we killed the boss the chest popped up and the ending dialogue appeared. Yet the mission complete did not, thus losing our loot.
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Make sure your fireteam jump down to the final boss arena one at a time.
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Bungie is aware. This usually occurs if the checkpoint doesn’t update after opening fake chest. If not in an extinguish version of the nightfall, you can wipe & it’ll reset everything back to normal.