A different kind of disturbing...
In Final Fantasy X-2 (a game that I enjoyed, in part because not so many people do), you have the main character, Yuna, being the target of the advances of another character named Brother. He's not Yuna's brother, but he is the brother of another character, Rikku. And Rikku's father is Yuna's uncle, as he was the brother of Yuna's father.
So... Brother is Yuna's cousin, and as I just spelled out, not a distant cousin.
And nowhere in that game was there ever a hint that Brother wasn't biologically related to Rikku... So... yeah...
But then you have the Honey Bee scenes in FF VII, so disturbing scenes are not new to the FF franchise.
And then in Mass Effect 3, there's a somewhat hidden bit about the fate of Joker's family. It's... what it is.