Giuseppe Sannino's first game in charge of the Hornets looked to be heading for a dull, goalless draw until the home side were awarded a penalty with 19 minutes remaining.
Referee Graham Scott pointed to the spot after Frank Nouble's cross appeared to strike Gabriele Angella on the arm.
But Scott was surrounded by furious Watford players, and their protests took several minutes to abate before David McGoldrick fired Ipswich ahead.
Joel Ekstrand was the only player booked for his excessive behaviour, but Sannino's side were reported to the FA after being accused of taking their protests too far.
A statement on the FA 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."
Troy Deeney equalised 11 minutes from time to snatch a point for Watford, who are now without a victory in their last 10 matches.