when a player shoots and gets cleaned out and the ref doesn't give a pen but will always give a foul outside the area

The other one I just don't get is when a player heads the ball and then another player heads him and they call it an accidental clash of heads

How is it any different to a late challenge - one player has won the ball albeit with his head and the other player has fouled him with a late challenge

Would you have given a penalty for the handball if it happened in a game you were refereeing ?
I wouldn't