This is a known issue that Bungie mentioned in the lastest "This week at Bungie" blog post. It happens if you reset your Valor, or Infamy, in the middle of working on those quests.
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Good to know! I probably missed that in my read. That said, the amount of Infamy required to clear Quid Pro Quo almost certainly shouldn't be a full reset I'd think. Am I mistaken about that?