The Portuguese’s anger stems from the European governing body hitting Phil Jones with a two-game ban for verbally abusing an anti-doping officer.
The England international was reportedly angry at being pulled away from the Red Devils’ celebration after beating Ajax in the Europa League final.
“I only hope tomorrow the team that wins, the doping control people allow them to celebrate and enjoy their moment,” Mourinho said.
The game in Macedonia will present a chance for Mourinho to assess the level of his side ahead of the new season.
But Mourinho has put distance between his side and Los Blancos, despite spending over £300m since joining the club last year, insisting that Zinedine Zidane’s side are on another level right now.
“We are going to try, that’s obvious but the difference between the Champions League winner and Europa League winner is also obvious,” Mourinho added.
“The top quality is in the Champions League, the semi finals usually have four of the best five or six teams in Europe.”