http://destiny.wikia.com/wiki/Crux_of_Crota
You need to have the eidolon equipped while killing crota?
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As far as I know, I was the only one in my last two raids that had an Eidolon Ally on me, and it wasn't equipped. The last node is only halfway upgraded. The guys who got The Crux, one from each of two HM raids played in rapid succession either did not even have a husk in the case of one, or hadn't even finished his husk of the pit yet or it wasn't a fully levelled Eidolon Ally.