Manchester United dominated the majority of possession in the first half but a lapse in concentration allowed Atletico Madrid the space to score the only goal of the game.
Before half-time, Antoine Griezmann surged down the right flank and sent a cross to Renan Lodi, who was unmarked on the opposite side.
Lodi had ample space around him and he found the back of the net.
However, Cristiano Ronaldo and some of his teammates felt that the goal should not have stood after Anthony Elanga came together with Reinildo Mandava in the build-up.
Arguably, that moment allowed Atletico to capitalize and score the goal but the referee allowed the strike to stand.
Ronaldo was livid and shared some heated exchanges with the referee. He then proceeded to hold an imaginary pair of glasses on his face to signal that perhaps the referee needed to get his eyesight checked.
The 0-1 defeat means United have crashed out of the Champions League while Atletico are through to the quarter-final.