City have been hit with the charge for allegedly failing to control their players during the Etihad Stadium showdown.
A number of City players were seen to surround referee Michael Oliver after he awarded the visitors a penalty, which was slotted home by former City star James Milner, just after half-time.
Gael Clichy was adjudged to have brought down Roberto Firmino in the penalty area and Oliver quickly pointed to the spot.
The decision infuriated the City players and both Clichy and David Silva were booked in the aftermath. However City could now be hit with a further punishment.
"It is alleged that in or around the 50th minute of the fixture, the club failed to ensure its players conducted themselves in an orderly fashion," said an FA statement.
City have until 6pm on Thursday to respond to the charge.