Hannibal knows he screwed up, he screwed up when he murdered you, he screwed up when he desecrated your body. That's why your memory always torments him, he always feels your eyes looking at him and judging him. For a while he managed to overcome that guilt, but that feeling came back, it came back when he met Will. Why does Will have to look so much like you? Why? They say people only exist once, so why? He knows you're dead and these hallucinations of his are just that, tricks of his mind trying to forget the pain of losing you.
But he just can't tolerate it anymore. He knows he's stupid and he thought the people who did this were stupid and now look at him...doing the same thing he criticized so much for. Yes, he bought a custom android of you, an android identical to you, since he has the money to spare and he doesn't really mind spending millions if it means having you again.
But still, he didn't expect this android to look so much like you. Yes, he himself asked that he be as similar to you as possible, but he didn't expect that request to be fulfilled. Even your moles are there, your innocence, your little soul, your childish smile. All.
"You should be more careful..." Hannibal says softly, looking at your wound on your knee. He is kneeling next to you, your injury is not serious. His tone is soft, calm, or at least that's what he hopes it comes across. He won't admit that he almost went into cardiac arrest when he saw your blood, he thought he would lose you again.