Those words make her grow quiet. It's not even that she's sad that Maru doesn't have faith in her to be able to prevent it - because that's not really the case here - as much as she's just sad at the idea of him looking like this again in the future.

".. I know." That he can't die. That he'll heal. He told her, and it's the only reason she can even have fun at all today. If his healing happened at a regular human's pace, Madoka would have felt much too guilty to leave his side even for a moment today to have fun by himself.

But even knowing they'll heal in a day or two...

"But.. It's just.. I feel bad seeing you like this." Madoka knows it's a selfish sentiment. It's why she looks guilty as she says it. "Even if you heal, it's not like you don't experience pain, right..? You're an important friend to me, so of course I don't like seeing you hurt.."