We dont have a clear answer, when mc talk with Wendy in the bathroom, he say "my father", so they don't have the same father. She could be adopted but that part about Wendy birth that break the family make it impossible . So it's either Maria having some african ancestor, cheating, rape or maybe something related to her work . (we also know that mc's father was very strict to wendy and that she has a lot of resentment towards him and that at a certain point Maria left with Wendy because circumstances demanded it.)
So if it's the cheating part that bothers you, you should give the game a chance because it's just a possibility and not a fact so far ^^