People, Wanda could have made Magneto no her parent just by unconsciously wishing it to be true, especially because her mind and morals were altered, it happened during the axist event in which the villains became good and the heroes became evil.

or the Magneto we have isnt her father, because the Magneto that was her father died in Genosha, and this Magneto is a creation of her from her crazy pre-mday days, because she couldnt tolerate the loss. so, in a way, it's true, she isnt his daughter, she is his creator.