See, Tony's reaction now only makes it all the more obvious to her that he was mostly just angry because he was worried. So Madoka easily lets him take her hand, even actually looking at him to meet his gaze. She tries to smile a little and nod, though it looks more than just a little forced - still lined with guilt for having caused her dad such worries in the first place.

But then there's Ignis too, and Madoka - uncharacteristically, compared to how happy she usually is to just throw herself at him the moment he says anything like that - seems to hesitate for a moment when he speaks up. It doesn't feel right to seek comfort when she's the one causing trouble, so instead of actually hugging him, Madoka just grabs the hand he's holding out with the free hand she's got left.

"Papa.. I'm sorry. I did something without asking first."

She does believe she did the right thing in the end by forming that bond with Maru. That's something she doesn't want to apologize for by itself - if not just for poor Maru's sake. He's not a mistake. But Madoka will at the very least admit her fault when it comes to the part she's apologizing for now.