Additionally, an "insufficient number of travelling stewards" mean the FA is accused of falling foul of UEFA's safety and security regulations.
UEFA's Control, Ethics and Disciplinary Body will deal with the case.
Elsewhere, UEFA is looking into salutes performed by Turkey's players during their matches against Albania and France – an apparent show of support for their country's military offensive in Kurdish-held regions in northern Syria.
European football's governing body prohibits provocative political statements inside stadiums.
UEFA said: "An Ethics and Disciplinary Inspector has been appointed to initiate disciplinary investigations with regard to potential provocative political behaviour by players of the national team of the Turkish Football Federation on the occasion of the 2020 European Championship Qualifying Round matches played against the national team of the Football Association of Albania on 11 October 2019 and the national team of the French Football Federation on 14 October 2019, respectively."