This happens a lot in the Cup, I see a lot of teams winning 4:0 the first match with no obvious advantage and then they eventually lose the second match, but still progress for obvious reasons.
It also happened to me last season - granted, I was playing a level 7 team while I myself was 4th, but I had a minor quality advantage. It was a managed team, but by a complete noob who didn't even level up that season and had finished 7th the previous one. Lost 0:4 at home the first match and half of my team got rated at 5 ... then the second match it was 0:3 for me by half time and finished 1:4 with them scoring in the last minute with their only shot on target. That was my only loss for the season in all competitions and it got me out of the cup, even though for most of the time it looked like I had turned it around. Now THAT sucks big time, but unfortunately it happens to a lot of people.