During the early stages of the clash, which saw City twice come from behind to salvage a point, QPR had two efforts disallowed by referee Mike Dean.
Charlie Austin's header was ruled out for offside after eight minutes and the striker was denied another goal in unusual circumstances soon after.
City goalkeeper Joe Hart touched the ball twice when taking a free-kick, meaning it had to be retaken after Austin had fired home.
A number of QPR players surrounded Dean following the two disallowed goals and the FA has decided to take action.
"Queens Park Rangers have been charged by The FA following their game against Manchester City on 8 November 2014," read a statement from the organisation.
"It is alleged that in or around the eighth minute of the fixture, the club failed to ensure its players conducted themselves in an orderly fashion."
QPR have until November 17 to respond to the charge.
