The Football Association has charged Burnley with failing to control their players in the FA Cup defeat to Arsenal earlier this month.
Kyle Lafferty was sent off at a crucial moment in the 2-0 loss for a foul on Brazilian midfielder Gilberto.
Alan Wiley's decision was not well received by Lafferty's team-mates and Burnley have now been charged with breaching Rule E20 (a), 'a failure to ensure its players conducted themselves in an orderly fashion'.
The Clarets have until 24th January to respond.
Meanwhile, Burnley striker Jay Rodriguez has joined Scottish First Division side Stirling Albion on loan until the end of the season.
The highly-rated 18-year-old will continue to train with Burnley during the week and travel north to play for Albion.
"This move will be good for Jay," Burnley boss Owen Coyle told the club's official website.
"It will give him valuable first-team experience and that will in turn make him a better player.
"In between Jay will continue to train with us each week and hopefully the deal will be beneficial to all parties."