Halsey dropped one of his cards in the ensuing melee and he subsequently mentioned the incident in his match report to the FA who have given the relegation-threatened Riverside club until Feb 4 to respond to the charge.
Boro - who have been linked with a move for Hull striker Marlon King - were hit with the charge as manager Gareth Southgate's No 2, Malcolm Crosby, issued a rallying call following the club's slide into the relegation zone.
"These are tough times for Gareth, he needs support and he's getting support and when we get through the problems we have now he will be a better and stronger manager," said the former Sunderland manager.
"All through this season our fans have been excellent and they've just got to keep getting behind us and backing the team. If you play well the fans will always get behind you, if you don't then you're going to have to expect a little bit of flak."