Cards are subjective, some refs are more lenient than others. CR7 should have been red carded against Iran (the other way around, it sure would ahve been a red) in Portugals last game (it might even changed the outcome). This is a typical show of bias towards a more famous player.
There is also the fact that refs can be biased against bigger players, they are (that's my opinion) likely to sanction more reeadily a foul comitted by a bigger player on a smaller on than the reverse.
Japan, in their first match, played one man up against against Colombia during the whole game, because of a Colombian brain lapse with a ridiculous handball, which means that they had no incentives to foul for the rest of the game in order to keep their numerical superiority.
Fouls or yellow cards are not always due to vicious play, sometimes their are tactical and necessary. That's why I think that this mode of selection is obviously very flawed (too much discretionnary power for the ref).
At the end of the day fair play to them, but what we've seen at the end of the Poland's game shows than this mode of selection is a little bit ridiculous and that allegedly "fair play" teams can be ruthlessly vicious