The Dutchman was a bystander for Ethan Pinnock's headed goal from a corner on the stroke of half-time after he was forced off to betreated for a head injury.
De Ligt was filmed abandoning his treatment and kicking a ball away in fury after Pinnock's goal while the bench descended into anarchy.
Erik ten Hag was bookedfor his argument with fourth official Gavin Ward and his assistant Ruud van Nistelrooy suffered the same fate after his animated protests towards him.
United's manager credited their second-half comeback via goals from Alejandro Garnacho and Rasmus Hojlund to their 'fury', with coach Darren Fletcher also reportedly having kicked off in the tunnel.
Erik ten Hag and Van Nistelrooy were booked for their reactions after being left with 10 men to defend the corner at the end of the first half, with De Ligt's head covered in blood
De Ligt had suffered a nasty head injury early in the game when he collided with the knee of Brentford forward Kevin Schade, leading to lengthy medical attention to stop the bleeding.
He had to come off for treatment on his blood-soaked head on two other occasions, one of which was just before half-time when Pinnock scored.
Boos rang around Old Trafford in annoyance that the set-piece had been allowed to go ahead by referee Samuel Barrott.
The venom was no weaker minutes after the goal. According to the Manchester Evening News, United coach Fletcher 'went ballistic' at fourth official Ward at half-time.
Ten Hag claimed Manchester United's 'mad and angry' players used the supposed injustice around Brentford's goal to inspire their comeback.
'We were mad at that, we were angry at half-time,' Ten Hag explained after their first Premier League victory in over a month.
'It was not perfect but we controlled the game. We didn't concede chances and felt it was an injustice to concede as we did.
'Every game we win is important and I think again this team you see the togetherness and the fighting spirit.
Asked specifically why he and his coaching staff were so irked by the insistence that a bleeding De Ligt was forced off three times for treatment, Ten Hag doubled down on his reasons.
'It was dry blood,' he said. 'So it was already treated and just dry blood so none of us understood why he was sent off. I went over and asked him.
'It was a huge moment as Brentford is very good at corners and when you miss one of your best headers of course you are disappointed.'