Several Hornets players were seen to surround referee Graham Scott to protest after he judged that Frank Nouble's cross had been handled in the penalty area by defender Gabriele Angella, with Joel Ekstrand booked for his excessive behaviour.
David McGoldrick duly tucked away the 73rd-minute spot-kick but Watford are now facing possible punishment for their actions.
An FA statement on their official website read: "Watford have been charged for failing to ensure its players conducted themselves in an orderly fashion and/or refrained from provocative behaviour.
"It follows an incident which occurred in or around the 71st minute of their game at Ipswich Town on 21 December 2013.
"The club has until 6pm on 30 December 2013 to respond to the charge."
Watford did hit back through Troy Deeney to claim a 1-1 draw against Town in what was new head coach Giuseppe Sannino's first match at the helm having taken over from Gianfranco Zola.