I am only level two but so far I would say it might be due to moral and condition and bonuses.
So someone changed the whole 11 well I would assume those that came in had very poor moral this would have a impact.

Here is a example I probably on think it is a good one because I won, but I was 2..0 down after the first leg of a cup game to a worse team.
For the second leg I put bonuses to the max increased the condition of all my players and boosted there moral if needed. I won 3..1