There's a brief pause, an inhale of air, and then: "I don't understand feeling like that."

It's not a denial of what he's saying. Madoka doesn't think he's lying about that, partially because she knows there's just bad people out there. But understanding them or how they think?

That's so far beyond a regular and kind girl like Madoka.

".. those people must not be able to feel guilty, or something like that.."