When the Hammers battled Gillingham in their Southern Group A match in October 26, Ajibola Alese, 20, was previously suspended after receiving two yellow cards in their previous two group games.
West Ham were however, punished with three pointed deduction and sent out of the tournament as a result of that.
The Premier League side will be replaced in the last 32 by League Two outfit, Colchester United.
In a statement, West Ham acknowledge the sanctions from the FA and EFL saying;
“Clubs are informed of on-field player disciplinary records and suspensions via the FA’s online portal and, despite this not identifying the suspension of the player concerned at the time and therefore the pertinent formal notification from the FA not being provided, the club notes the decisions reached and await the full written reasons.”