The problem isn't that the author didn't think about just the weakness of the skeletal structure. It's that it took her reaction for the "smart" MC to notice or even think about it. I'd think that this analytical kid would be keen on recognizing weaknesses in others' powers because he appears to be in an unknown and precarious situation, especially when that power is as seemingly convenient as super strength.
That's what the author didn't think about. If he had sold us a moderately dumber MC from the start, it wouldn't be worth badgering over (though you could still question why he'd delay the reaction for one chapter, but it could be reasoned out).
But then again, I'd say he's selling me a moderately dumber MC right now based on what he thinks of - or doesn't think of - in situations like this anyway.