The Hammers' 3-0 defeat was overshadowed by pitch invasions, fighting among fans and an angry mob confronting the club's directors at the London Stadium.
Co-chairman David Sullivan was struck on the frame of his glasses by a coin hurled by the yobs below his seat.
Sullivan and vice-chair Karren Brady were asked to leave the directors box for their own safety. Sullivan was moved several rows back from his normal seat in the VIP area at the next home game.
The FA has been deliberating over a suitable punishment since the game on March 10 which represented a low point in the club's turbulent season.
The team recovered enough in the remaining weeks to finish 13th but the incidents have been hanging over their heads ever since.
At one point West Ham skipper Mark Noble fought with a pitch invader in the middle of the pitch and had to be restrained by team-mates.
The FA could hit West Ham with a heavy fine and even force them to play a game behind closed doors at their controversial 60,000 seater stadium.
West Ham are expecting a formal announcement of the charges later today.
The Hammers will defend themselves against the charge and have already moved swiftly to root out some of the troublemakers from the day and issued them with lifetime bans.
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While they also believe that the London Stadium operators were at fault for the crowd trouble during the Clarets, after they handled the incident poorly.
The 2006 FA Cup runners-up kick-off the new season with an away clash against Liverpool, before facing Bournemouth at home on August 18.
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