The loss saw Villa miss out on Champions League football next season and came after Morgan Rogers saw a goal ruled out, when the game was goal-less, after referee Thomas Bramall blew his whistle before the ball crossed the line.
Rogers had pounced when United keeper Altay Bayindir appeared to fumble but the official’s early whistle meant VAR was powerless to overturn the decision.
Goals from Amad Diallo and Christian Eriksen then condemned Villa, for whom a draw would have been enough to secure a top-five finish, to defeat and a place in the Europa League next term.
Emery confirmed Bramall, who has refereed in the Premier League for three seasons but officiated around half his matches in the Championship this term, had later acknowledged his error but the club’s sense of injustice was clear to see.
Director of football operations, Damian Vidagany, confirmed the club would be lodging a complaint after the post-match press conference.
Emery said: “The key moment, of course, was the goal of Morgan Rogers and how the referee in that moment decided this action.
“He whistled and of course he needed to have it under his control, waiting for VAR because VAR is coming for him.
“I spoke with the referee and he knows his mistakes.
“That is normal. I make mistakes every day, I made mistakes as well and the players are making mistakes on the field and sometimes the referee.
“We have to accept the mistakes. I think we have very good referees in the Premier League but sometimes they are making mistakes.”
Asked of Bramall had apologised, Emery replied: “It is not necessary. He knows, he knows immediately he made a mistake.”
Emery had no issue with Bramall’s decision to send off Emi Martinez for barging into United striker Rasmus Hojlund in first half stoppage time.
And while believing his team got the rough end of the stick when it came to the decision-making, he acknowledged they did not deserve anything from the match.
He said: “It (the Rogers goal) was a key moment. Maybe through this goal we could have got a better position, making the Champions League.
“But we didn’t deserve it, playing like we did.”