In the first intro mission, after Marcus gets through parts of CTOS that other hackers couldn't, Sitara claims that it's like he has reached "the secret cow level". This is a reference the infamous secret cow levels from the Diablo series.
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A PSN player, Goron2000, received a temporary ban for sharing on Twitter an in game screenshot that showed a fully rendered and hidden vagina after accidentally discovering it. Ubisoft created a patch to cover the vagina of one particular NPC, but interestingly left penises in the game. The player's ban was eventually lifted after several gaming news sources attempted to contact Sony for comment.