Mourinho nearly threw away all those gains with a series of errors during the clash with the Greek side, chief among them a call involving Brazilian winger Vinicius Junior.
It started with Vinicius returning to the starting line-up on the left wing, even though the team had looked sharper without him in recent matches.
The real problem ran deeper. Vinicius's inclusion pushed Ivorian Yan Diomande out to the right, despite his outstanding form on the left flank of late.
Madrid's attack duly fell apart on both wings. Vinicius offered nothing to justify his place on the left, while Diomande never found his best level on the right.