One of the first questions we often get from a new student is how to make a proper fist. Here's me in my backyard talking about it.
I have no idea why I look so mad in the first frame, or why I'm talking like a robot when my thumb is extended (??).
The book I reference, The Armored Rose by Tobi Beck is out of print, but you can get it used on Amazon. Its the only book I've ever read that discusses the inability of some people to make a fist with a flat top, but its not uncommon to have a student facing that situation. The most common explanation I hear is that the trainee has long fingernails, but I usually look to the bones in the hand for the answer first.
The doctor I talked to about it didn't know if it would damage the hand to hit with a fist made with one or two knuckles sticking up, as if you were frogging someone. If I can get a definitive answer from a hand specialist, I'll post their answer.