James was shown a red card for a goal-line handball, but the Blues' squad was enraged with the referee's decision as they felt the ball had deflected off the England star's thigh onto his arm.
"Chelsea FC has been charged with two breaches of FA Rule E20.1 following their Premier League fixture against Liverpool FC on Saturday," read an FA statement.
"It is alleged that Chelsea FC failed to ensure its players conducted themselves in an orderly fashion during the 48th minute of the first half, and following the half-time whistle. Chelsea FC has until Friday to provide a response to this charge."
According to the Daily Star, Chelsea will be hit with a heavy fine if found guilty of the charge, but speaking after the game, captain Cesar Azpilicueta insisted his side had done nothing wrong.
“The referee gets the information and goes to the VAR and just sees one image and it's enough for him to give a penalty and the red card,” he said. "But then we got two yellow cards for our defensive guys. We were just talking and I think it's good we can talk to the referees and they can explain the situation.”