A succession of pitch invaders attempted to reach Juventus forward Cristiano Ronaldo during the match and after the final whistle.
Ronaldo, who was returning to United for the second time since leaving 2009, took a selfie with one of them.
It is the second time United have been charged by Uefa this season.
They were fined 15,000 euros (£13,203) for the late kick-off of their match with Valencia at Old Trafford last month.
Uefa’s disciplinary body will hear the latest case on 22 November.