I thought the aunt did that behind his back, color me confused

She did. She stole the embryo and let the child grow until its born WITHOUT anyones consent.

However the male lead was already aware that yiyis embryo was stolen even in early chapter but doesnt know who stole it

I nearly forgot about this because it was chapters ago. I hope it doesn't take that long to get the baby back! My rage for the aunt keeps growing every chapter she's in!