The Red Devils needed an extra time goal from substitute McTominay to break the deadlock and get into the FA Cup quarter-finals.
When McTominay went off to celebrate the goal, Bruno joked that Marcus Rashford's pass was intended for him, not the Scotsman.
The mic picked up Fernandes saying "Hey, that ball was for me, motherf*****," to McTominay during the celebrations.
The Portuguese was speaking in jest after McTominay gave his side the lead.
United will find out their quarter-final opponent after the draw on Thursday.