Just found out that wearing or equipping a class item (Warlock Bond) that the Cryptarch gave you, increases or gives extra reputation when handing him your engrams
While I was wearing a Warlock Bond that he gave me a while back from an Engram he once decrypted, I was turning in other engrams and was receiving bonus reputation to the Cryptarch rank.
Probably already mentioned before, oh whale~
*Note: The warbond worn was "Born of Sight" with no level limit. (rare)
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Ur sure its not because you did nightfall?