United lost 2-0 on the day with goals coming from Virgil van Dijk and Mohamed Salah at Anfield.
The incident that necessitated the charge occurred in the 26th minute when the visiting players surrounded referee Craig Pawson for initially allowing Roberto Firmino’s goal to stand following a challenge on goalkeeper David De Gea by Van Dijk.
De Gea led the protests and was joined in by the likes of skipper Harry Maguire, Luke Shaw, Andreas Perreira and Fred.
The goal was however chalked off following a Video Assistant Referee (VAR) review but De Gea was cautioned for his involvement in the incident.
A statement from the FA read: "Manchester United FC has been charged with a breach of FA Rule E20(a).
"It is alleged that the club failed to ensure its players conducted themselves in an orderly fashion during the 26th minute of the Premier League fixture against Liverpool FC on Sunday (19/1/20)."
Ole Gunnar Solskjaer’s side have until Thursday to respond to the charge.
"Maybe I shouldn't talk too much about that," Solskjaer said when asked about the charge in Tuesday’s press conference ahead of the Premier League home game against Burnley on Wednesday.
"Let's get that decision done. It's overturned [the decision]. I reacted myself because it was a foul."
United remain fifth on the league log ahead of the visit of Sean Dyche’s men.
