Arsenal have been charged for failing to control their players, who surrounded referee Michael Oliver when Myles Lewis-Skelly was controversially sent off on Saturday during their 1-0 away win at Wolverhampton Wanderers in the Premier League.
Arsenal players protested the decision, which was overturned earlier this week following an appeal.
Oliver dismissed Lewis-Skelly for tripping Matt Doherty on the edge of the Wolves box before half-time and the video assistant referee upheld the decision.
After Arsenal provided clips of the incident as evidence, an independent commission overturned the red card, lifting his three-match ban.
"The referee had made an obvious error in sending off Lewis-Skelly for the challenge that he had made," the independent commission said.
Oliver's call was also criticised by fans and pundits, with referee Oliver receiving threats and abuse which prompted a police investigation.
Arsenal have until Monday to provide a response, the FA said.