Madoka is about to ramble off a list of excuses and potential solutions, but before she can even get started on the first one, he's suddenly dropping back like that. And the words that follow make all the words die in her throat straight away. Instead Madoka just quietly stares at him for a moment, the panicked expression from a moment ago turning into something more thoughtful.

"You.. don't think that I'm not comfortable with you, right..?" Because it'd make her feel bad. She definitely doesn't want to give off that impression. "Because that's not the case at all! You're really sweet, and really smart, and you say such nice and insightful things to me.. You've been really helpful with my problems before, and it kind of makes me feel like I can talk to you about those kinds of things."

She's entrusted him with a lot more than she has with most people, after all. And she even fell asleep against him when he offered to let her stay that one time. She wouldn't do any of those things if she wasn't comfortable with him.

"The 'mister' thing.. i-it probably sounds strange, but it doesn't have much to do with that, I think.. It's a problem with me, not with you." Because she lacks self esteem. There's no way Madoka can allow herself to be impolite with people when she doesn't think she has the right to be. It's hard to tell whether she consciously realises to that extent that that's the problem.