FA Rule E20 explains an organisation's responsibility for ensuring that its members behave appropriately. It states that: 

Each Affiliated Association, Competition and Club shall be responsible for ensuring:

(a) that its directors, players, officials, employees, servants, representatives, spectators, and all persons purporting to be its supporters or followers, conduct themselves in an orderly fashion and refrain from any one or combination of the following: improper, violent, threatening, abusive, indecent, insulting or provocative words or behaviour, (including, without limitation, where any such conduct, words or behaviour includes a reference, whether express or implied, to any one or more of ethnic origin, colour, race, nationality, religion or belief, gender, gender reassignment, sexual orientation or disability) whilst attending at or taking part in a Match in which it is involved, whether on its own ground or elsewhere; and 

(b) that no spectators or unauthorised persons are permitted to encroach onto the pitch area, save for reasons of crowd safety, or to throw missiles, bottles or other potentially harmful or dangerous objects at or on to the pitch.

If a County FA believes that a Club's members have not behaved appropriately they may raise a misconduct charge against the Club. The most common examples of this would be if there is a mass confrontation between players during a game, or if spectators behave inappropriately.

When a Club hits a certain threshold of offences during the course of a season they may also receive a charge under FA Rule E20.