I think I mentioned this somewhere else but its to do with squad sizes, I think its currently 32 will be 25 for next season. too many players = training ground injuries. injuries are on a 5% chance and they system checks best player to worse player, so your good players are more likely to get injured.
but i will check the percentages to see if i can see why its always those 2 guys in your case, but you may just have been unlucky to get the same 2 injured more reg than anybody else. will check.