Busquets appeared to handle the ball in the area during the dying seconds of the Rojiblancos' 2-1 loss at the Vicente Calderon but match official Perez Lasa waved away the home side's appeals for a penalty.
Falcao believes that the Barca midfielder's offence was obvious and appeared to call the integrity of the referee into question in a post on his Twitter account on Monday.
"I think the only person who didn't see Busquets' handball yesterday [Sunday] was the referee," the Colombia international wrote. "Can it be that he really didn't see it?"
Atletico boss Diego Simeone was also bemused by Lasa's failure to spot the Busquets handball, as well as his decision not to send Dani Alves off when the Brazilian pulled down Felipe Luis midway through the second half.
"The referee was perfect, although there were little things," the Argentine coach told reporters after the game.
After suffering their first defeat since the arrival of Simeone during the winter break, Atletico will now be hoping to bounce back when they face Sevilla next weekend.
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