To be fair City's set up was miles away from what it is now under Pep.
Pep's favoured line up is essentially suicidal. Nolito, De Bruyne, Silva and Sterling in a 4 behind the striker, with only Fernandinho covering the very mediocre defensive unit. A quality counter attacking side would shred them to pieces, which is obviously what Jose was thinking today, he just called the team selection totally wrong on the wings, favouring work rate (and i think he's totally wrong about Lingard having better work rate than Rashford) over quality on the ball.
Mkhitaryan is quality on the ball on the edge of the opponents box, not on the half way line surrounded by 3-4 City players.