Well, at the beginning of the MLS there were some differences between US and FIFA rules. The 2 main differences were:

1. clock counting down - the clock would stop whenever not in play (just like in basketball), and count down to 0:00.

2. penalty shootout - since the americans were thought to not accept sports in which a game can be tied, they decided to tiebreak every league game by a weird penalty shootout - they put the ball 35 yards from the goal, and the player had 5 seconds to score, 1 on 1 against the keeper.

both weird rules were changed in 1999 and 2000, and now they are compatible with the world federation rules.