Why do some people punch with their thumbs in?

thumb inside the fist is a bad idea, its a great way to break your thumb

the position of the thumb changes the strength of the wrist.

if you put your thumb on the side of your fist it makes your wrist stronger, when you put your thumb on the out side across your fingers it starts to weaken your wrist, the further access the weaker the wrist

you can easily see this when someone puts you in a wrist lock.

the best think to do is to make the fist the way your instructor tells you, there are several variations, all having there advantages and disadvantages, some more then others. but inside the clench fist is never a good idea, i can think of any advantage too that one

You will break your thumbs, this is a bad idea.

Yeah, I do it

If you don't and you come to a real fight you could lose or break one of your thumbs : (

also it can strengthen your hit as the thumb fills in the empty space : )

Never punch with your thumbs in! I dunno who told you that but they obviously never tried it. You can break your thumbs.