To be honest - he isn't doing that to make you feel bad - he obviously DID get hurt and since you said this was the 2nd time....please be careful -
I don't want to scare you but small dogs can die from being stepped on. someone right here lost their little puppy when her boyfriend stepped on him
What I would do is try to keep him away from anything until he gets big enough to get out of the way by himself.
I hope he's ok - but when they cry like that .....they're telling you something. Poor baby.