Ralf Rangnick's side struggled to compete in what was a typical Atletico Madrid performance.
Atletico took a first-half lead and with the way they can frustrate, the result never felt like it was going to change.
But Rangnick has said he is curious about some of the referee's decisions on the night.
"He made it easy for Atletico to time-waste"
Many footballing fans will detest the way Simeone sets his teams up but it is effective and has proved its worth once again.
"There were some curious refereeing decisions. I wouldn't say they were decisive, bar maybe the one before the goal. He made it easy for Atletico to time-waste," Rangnick said after the match.
"In the second-half, I don't know if the game was played for more than two minutes without being interrupted by someone lying on the floor."
The United interim was then asked whether he side were 'naive' against Simeone.
"I don't know about naive. We were against Atletico - the champions of that style of football. We didn't always take the right solution around the box.
"I think we played a good first half, all those things we planned to do, we did. Against a team like Atletico, it is highly important you score first.
"We conceded in a transitional moment. I believe a foul on Elanga. The linesman and referee didn't see that," he added.
But Rangnick said it himself, against Atletico, teams cannot expect to create clear-cut chances and enjoy a free-flowing game when going behind.
United did exactly that in both legs.
In Madrid, it was Lodi who whipped in a cross for Joao Felix to head home and in Manchester, it was Lodi at the back post to head past De Gea and win the tie. Both were first-half goals and what followed was simply copy and paste.
Rangnick’s side were lucky in the first leg and had Jan Oblak been positioned correctly, United would not have equalised.
As United were eliminated, it means they have now gone five seasons without winning a trophy which is the first time since the 1970s.