The fact they scored on a counter attack seems a little odd, but was it really a counter attack? I have seen the commentary say counter attack a few times when it clearly was not.
I fail to see what the real issue is with this however. IRL just because a manager instructs his players to form an ultra defensive does not mean they will not conceed. The players still need to make the plays and mistakes do happen. And sometimes there is just nothing you can do about it, a bad bounce, and great play by the other club, etc....**** happens