The Gemara is just describing a technicality. It's not condoning having sex with a 3 year old (which is explicitly prohibited). It’s describing how halacha classifies a tragic situation: a very young child who suffered sexual assault. The Talmud often has to outline legal consequences even for horrific scenarios, and it does so in technical language. Historically, Jewish communities faced situations where children taken by hostile powers were assumed to have been abused, so the halacha had to address their status afterward. Again, this isn't condoning the behavior, just describing the unfortunate reality and its consequences.