Los Blancos were the better side and deserved their victory, as Casemiro, Sergio Ramos and Gareth Bale got the goals, rendering Antoine Griezmann's effort insignificant.
Although coach Diego Simeone insisted in his post-match news conference that VAR was not to blame for the defeat, Atletico players were angered by several contentious calls during the game, which the club has attempted to shine a light on.
The first controversial moment was the decision to award Madrid a penalty when Jose Gimenez tripped Vinicius Junior on the left side of the box, with VAR officials backing referee Javier Estrada Fernandez pointing to the spot.
However, the screenshot of the incident that Atletico uploaded on Twitter appears to display contact first occurring outside the area.
Simeone's men were then denied an equaliser when Alvaro Morata was deemed to be offside before beating Thibaut Courtois, but the club's post seems to show the former Madrid striker being played onside by Ramos.
Morata was also involved in the third incident, not getting a penalty despite Casemiro appearing to make contact with him in the box, as Atletico attempted to highlight in its final image.