If a system is failing that counters the oppositions attack it's usually just the game engine having it's way with you.
If it happens all the time against the same formation something is wrong with your orders, the only way to rectify this is by tweaking them slightly as you never know what the opponents orders are, the game engine gives you clues as to how he is playing, IE. ST (a) passes short to ST (b) or DC/DR/DL/DMC hits long ball up field all through the game.
Last night I changed orders four times, on paper I should have won comfortable, I had almost 70% possession away, no joy, 1-0 defeat, sometimes you have to accept, the game engine wins, not your opponent.