I just completed the Nightfall for Insight Terminus with a score of over 80,000 and I didn't get credit for 3 different quests I have asking me to complete Nightfalls. Map fragment - 0/3, The Essence - 30/50 when we started and no increase, Band Together - not completed.
I know our modifier might not have been high enough for one of the quests. But to not get credit on any one of them is troubling.
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Did you leave to orbit after you picked up the chest? If so, the mission complete timer doesn't start until ghost finishes his dialogue. If you leave before the timer appears, the activity will count as incomplete.