It’s not that Illya doesn’t understand what she means, from a logical standpoint. Clint believes she’s a good person, or he believes she at least has the potential to be. She wants to be the person Clint believes her to be, but she believes herself to be rotten inside for some reason Illya still cannot understand. He gets that much, he can understand her up to that point.

It’s just that he has a hard time understanding from an emotional point of view. He’s spent so measuring his life worth through the eyes of someone else, it’s just hard for him to imagine living his life otherwise. Which was probably her point, earlier. A point he may agree with, but he isn’t quite ready to fully accept.

He reaches to touch his father’s watch, hoping she won’t notice. If she asks about it he won’t be able to lie to her.

“I don’t believe in just trying. Either you do or you don’t. But I don’t really understand what makes you a good person. Or what makes you person. I thought doing what I was supposed to do, following orders and cleaning my family’s name would make me a good person.” He doesn’t sound like he’s fighting it anymore. Honestly, of all the things he could talk about this is comparatively harmless so it’s better if she keeps her on this track of thought.

“I am not sure anymore.”