United were leading 2-0 at Old Trafford thanks to two goals from Fernandes when Rashford was brought down in the penalty area.
Being the regular penalty-taker and on a hat-trick, every onlooker expected the Portuguese to step forward and look to convert from 12 yards.
However, it was Rashford who was given the responsibility and the England forward duly slotted the ball home, with United going on to win 4-1.
While it proved a successful move, former Blackburn and Chelsea striker Sutton felt it was strange and questioned why Fernandes would be handing penalty duties to anyone else.
‘That’s odd,’ Sutton told BT Sport. ‘That’s odd because ultimately the manager is the one who, or should, make the decision on who takes the penalties and Bruno Fernandes isn’t the manager.
‘That’s the way it should be. You can’t imagine under Sir Alex [Ferguson] it happening with him.
‘Ultimately, it didn’t matter tonight but in a tight game if United don’t end up winning the game it ends up becoming a huge problem.’
The Portuguese saw a spot-kick saved against West Brom at the weekend, but it was retaken due to the goalkeeper being off his line and he scored at the second attempt. He revealed on Tuesday night that after that match he had told Rashford he would be next up from the spot.
‘Of course, everyone wants to score a hat-trick but after the game in the Premier League [against West Brom] I told Rashy the next one he will take,’ said Fernandes.
‘I remembered that and also because he is one of the top scorers in the Champions League.
‘I think it will be important for him to keep going there and taking that confidence.
‘As I say, it doesn’t matter who takes the penalties. The most important thing is scoring and the team scores. When the team scored I score too.’
Rashford has now scored five goals in the Champions League this season, only behind Borussia Dortmund’s Erling Haaland on six.