The France international, who captained United against the Swiss champions, limped off in the 3-0 win and some reports have suggested he could be out for 12 weeks with a muscle tear.
But manager Jose Mourinho has said the nature of the injury would not be known until after the results of the scans.
United thumped Everton 4-0 over the weekend with Marouane Fellaini stepping in for Pogba but Mkhitaryan said the club would miss Pogba's creativity that has help them script big victories this season.
"It's hard, because he's a top player for us," he told France's SFR Sport. "It's going to be very difficult, but the coach knows how to make up for that and we're going to help him come back stronger."
Mourinho's side share top spot in the Premier League table with Manchester City and have 13 points from five games. Both Manchester clubs have scored 16 goals and conceded only two.
United host Championship side (second tier) Burton Albion in the third round of the League Cup on Wednesday before travelling to Southampton in the league on Saturday.
(Reporting by Shrivathsa Sridhar in Bengaluru; editing by Sudipto Ganguly)
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