criss - there you have it - yet another hole in the famous 'Swiss Cheese' aviation accident model - NB no sick humour intended there.
Life is always full of surprises, not all of them nice, and it is just a terribly sad thing that these things (as with the 'procedures' in place in ATC) only come to light in these tragic circumstances. If you go through any procedures anywhere with a fine tooth-comb it is likely you will find other 'contradictions'. It was the combination of 'holes' there that sadly made this a fatal event. 50-100' difference and there would have been a load of people alive but severely frightened and the holes would have been closed.
The best we can say out of all this is that a few more 'holes' have been shut. I do not mean to sound trite, but it is not a perfect world.