The players of the club were charged with failing to control their players after an injury-time incident in the game against the Blues.
The referee awarded a late spot-kick after Antonio Rudiger was brought down in the box.
The FA said in a statement that it had charged the team with a violation of FA Rule E20.1 after the match.
It is alleged that the players of the team did not conduct themselves in an orderly fashion when they surrounded the referee in the 93rd minute.
The charge has been given until Thursday to respond to.
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There are free to watch highlights from the game.
Five players were booked for the game, which ended in a heated exchange between the players and the referee.
Raphinha scored from the spot in the 28th minute to give the visitors a lead.
The two second-half penalties were for fouls on Rudiger. The second came in the last moments of the game when Klich barged into the back of the defender.
Sky Sports News spoke to a former referee who said it was a penalty.
The player goes through the back of the player, it's a foul, and there is no need to make the tackle, Rudiger does what he should do, he gets between the player and the ball, and the player goes through the back of him, it's a foul
Seven of the players in the top flight are one booking away from suspension, and that's the worst record in the top flight.
