Kompany, 31, made the 2,000 mile trip to Kharkiv this week with the rest of the City squad after being rested in the 2-1 victory over West Ham United on Sunday (3 December) – with Pep Guardiola perhaps also choosing to take him out of the firing line having collected four bookings this season.
The skipper was expected to start at the heart of defence in City's final group game on Wednesday but was instead a notable omission from the squad, with midfielder Fernandinho dropping back to partner Eliaquim Mangala as the Premier League leaders suffered their first defeat of the season.
Kompany's omission will spark fears over his availability for the trip to Old Trafford on Sunday. Guardiola explained post-match: "Kompany didn't feel good," the Manchester Evening News report. "I wanted to make him play, but he didn't feel good so it was an opportunity for the others to play."
Fabaian Delph was another notable absentee on Wednesday night. The former Leeds United starlet has impressed on the left in the absence of Benjamin Mendy and was set to start against Paulo Fonseca's side only to be ruled out by illness.
"Fabian Delph was going to play but vomited yesterday," Guardiola said.
Nicolas Otamendi and Kyle Walker meanwhile both travelled and were named on the bench but were not called upon by their manager.
David Silva meanwhile did not make the trip to Ukraine. The Spain international suffered a knock after scoring the winner against David Moyes' side last Sunday with Guardiola revealing earlier this week the decision to leave him back in Manchester was an enforced one.
"David Silva has a little problem – I don't know whether he will recover for Sunday," Guardiola said. "He felt uncomfortable after his goal [against West Ham]. He felt something. Hopefully he can play on Sunday."
Manchester United meanwhile will be without Paul Pogba, who will begin a three-match ban on Sunday. Mourinho could also be without Phil Jones and Eric Bailly, who have not featured since before November's international break.