He never meant to leave her hurting with that reply. Of course not. It was more so that he was stating a plain fact. However in retrospect, he realized maybe he should have chosen a different way to word it all.
Also (almost) at the tip of his tongue was to say that Kaito really is a good person after all, isn't he? But he knew she would stick to her opinion. That was fine.
"It's just how it was," he replied quietly. Naturally it hadn't been something he would have asked for, but life did that kind of thing. Again, too, he wouldn't blame Yuuki for anything.
One of his hands slips over hers. "I'm here, now, and am fine, aren't I? That's the part that matters."