Of course Madoka believes he genuinely means it when he says there's nothing wrong with it. But for some reason - honestly, it's probably just little kid instinct - she can't help but stand a bit more on her toes to try and make herself seem the tiniest bit taller all the same. Even though she should probably realise it'll be so obvious she's doing that if he can feel his hand going a bit higher...

"I want to be a bit taller though. My friends back home were-- are all taller than me too. I have to grow taller too so I can be a more dependable person."

Yes, she knows dependability doesn't have much to do with height, but.. still! A few more inches couldn't hurt, right? It's harder to help others when you're a pocket girl!

"Mister Gladio, do chocolate cupcakes help you grow taller?" Apparently she hasn't forgotten her purpose for them coming back to the train. "I'll eat them all!"