I think this comes from the English Lucretia dialogue, actually. I'm not sure how it is in Japanese, but after a series of scenes implying a heavy romantic tryst between Vincent and Dr. Crescent, Lucretia reveals she is pregnant and that the baby will be part of Hojo's work. (If I recall correctly, this is sometime after said tryst comes to an end) When Vincent expresses outrage, Lucretia pointedly says that it's her choice, because "It's not as if the father is around".
My understanding is that she only said this to hurt him though, and that according to the original FFVII canon Hojo is the father. Then again, the Ultimania also disagrees with the game and says that Hojo drugged her into participating in his experiments while the game shows her to be a lucid, willing participant.
It's likely the result of the DoC team forgetting that they'd already made a canon statement about the paternity.