Remember that this game is programmed by humans, and it seems that they are not as knowledgeable about football as we would expect them to be for people who run a football manager game.

All I can say is this: you cant win them all. There is more randomness in this game than in the real world at times. What I mean by that is that impossible results, or more like unlikely results happen more often in this game than one would realistically expect. Most times there is no reason why a result happens other than the computer chose a result from its matrix and it went against you even when everything was in your favour. I use the term "anti-lottery" since its basically winning a negative prize. You rolled the proverbial "dice" and rolled snake-eyes and got a troll result against you.

Even when you have players at 99% condition and morale, playing a perfect counter formation with perfect instructions against a much weaker team, this game will troll you because you won the anti-lottery when it chose the result from the matrix. Your in-game changes did not change the result it had already chosen since your changes were not enough to sway it from its original choice.