Most of the time, if not every time, I do the Nexus bounty it doesn't register upon completion. If I do it a second time it usually takes...
Fix?
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Been a known bug since day 1. It's in the help section somewhere. Bungie's only answer is "Do it again".
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I know it won't count if the boss dies and it's been 30 seconds or more since you damaged it.
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Bump And it's not just nexus, I've had that happen on devils lair too