How are you mystified by this concept? Sex should involve both parties agreeing that they are okay with what is going on. This also includes fertilization without sex. I, and no other male who has ever lived or will ever live, doesn’t have the right to just make a woman have my child without her agreeing. Mary did not consent to any of this in the story. It is rape.
Good thing not a single aspect of the story occurred. Every nativity scene you have seen in your life depicts the fictional story of a woman raped. Maybe I shouldn’t have used the word woman given her age and should have said girl instead given her age.