I got a new Husk of the Pit today and grinded it up to an Eidolon Ally and it says it still needs a crux of crota to upgrade? It also didn't start the exotic quest line for me.
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Are you sure you have the new one? Does it have the Iron Lord axe icon on it? Here are the quest objectives: Get the Husk of the Pit drop from Hive enemies or Nightfall Farm Thrall, Wizards of Knights to get the Eidolon Ally rifle Visit the Speaker and Eris at the Tower Complete the 390 version of Crota's End, defeat Omnigul in The Will of Crota Strike Use 'Essence of the Oversoul' item Eris gives you on the Eidolon Alley to get the Necrochasm If that helps.