In March, Atletico was fined 10,000 euros ($13,600) by UEFA for incidents at a Youth League match against Manchester City. UEFA also ordered Atletico's stadium to be partially closed for its next home match in that competition.
Atletico fans were also implicated in making monkey noises at Levante midfielder Papakouly Diop during a league match this month.
Diop answered the taunts by doing a dance, which enraged the traveling Atletico fans at Ciutat de Valencia stadium after a 2-0 loss.
"I started to do the dance to take importance away (from the jeers)," Diop, who is from Senegal, said then. "That they call black players monkeys has to end."
In the highest profile case, Barcelona defender Dani Alves responded to a Villarreal fan who threw a banana at him last month by eating the piece of fruit before continuing to play.
The Spanish league fined Villarreal 12,000 euros ($16,000).