UEFA's Control, Ethics and Disciplinary Body charged the Merseyside club with "aggressions by supporters against players" under Article 16 (2) of its disciplinary regulations.
Everton's hopes of qualifying for the Europa League knockout stages was ended by a 3-0 defeat in the reverse fixture in Lyon earlier this month, leaving them bottom of Group E with one point from four games.
Everton, who are struggling in the Premier League, sacked Dutch manager Ronald Koeman last month and have yet to appoint a full-time replacement at Goodison Park.
(Reporting by Hardik Vyas in Bengaluru; Editing by Ken Ferris)
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