Forest Green and Colchester have both been charged with failing to control their players during last week's league game at the New Lawn.
Players from both sides strongly protested following Forest Green midfielder Ebou Adams' challenge on Josh Doherty just before half-time.
Adams was sent off, but his straight red card was rescinded by the Football Association earlier this week following Rovers' successful appeal.
An FA statement said: "Forest Green Rovers FC and Colchester United FC have been charged with a breach of FA Rule E20 following their EFL League Two game on Saturday (27/02/2021).
"Both clubs allegedly failed to ensure that their players conducted themselves in an orderly fashion during the 45th minute of the game and they have until Monday (08/03/21) to provide their respective responses."
Forest Green, who won the Sky Bet League Two game 3-0, are currently third in the table, while Colchester are 20th, 10 points above the relegation zone.
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