Wanderers and Doncaster Rovers have both been handed an FA charge following the recent game at the University of Bolton Stadium.
Both clubs have been charged with a breach of FA Rule E20.1.
It is alleged that the clubs failed to ensure their players conducted themselves in an orderly fashion during the 44th minute of the game which Wanderers won 3-0 following the dismissal of Doncaster defender Joe Olowu.
Both clubs have until Wednesday 1 December to respond.