Something I've noticed with World Cups in general and I'm not sure what the answer is.
In general it seems to me that the opening round matches with the mini-leagues are quite well refereed (ie they all get together before the start and agree to sing from the same sheet). Of course the 3rd match in the mini-series can get quite heated. Fast forward to the semi final and final, and these go to very experienced referees at this level.
Now the difficilty is that with the start of the knock-out phases, teams are getting more desperate, but FIFA are trying to give refs more experience so they can be the guys who can do the late stages in future competitions. Thus you have a mix of teams getting pretty desperate at the same time as you have refs trying to get experience which can lead to the kind of situation we saw Tuesday.
I'm not sure what the answer is, because as we saw with our lads taking penalties, you can only get real experience with games that matter.