He can't help but blush a little, which he covers with a frown. Bruce's mentioning that he hadn't hit puberty was annoying in two ways;

One it reminded him that he still hadn't hit it, when everyone else his age had started long ago, or at least this term.
Two for some reason, Tony had taken this to mean that Bruce wasn't seeing him as a 'man' yet. Which bothered him, as much as the fact that realising this was what caused him to blush in the first place.

"Who says I haven't hit it? My body's just taking it in a more subtle and dignified way compared to everyone else. It's not that surprising."

He scratches his cheek as he talks to hide his face casually.