The misconduct charge relates to City's complaints after Liverpool were awarded a penalty 50 minutes into Sunday's 1-1 Premier League draw between the two sides.
The hosts' players – including Yaya Toure and David Silva - fumed at referee Michael Oliver after Gael Clichy was adjudged to have fouled Roberto Firmino with a high boot in the box.
James Milner subsequently scored from the spot, before Sergio Aguero's equaliser earned a point for City at Eithad Stadium.
"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," read the FA's statement.
Pep Guardiola's men have until 18:00 GMT on Thursday to respond.