The clubs met in the league for the first time last season, with AFC Wimbledon failing to recognise the MK Dons name in their opening meeting at the Cherry Red Records Stadium back in March.
In September's game in Kingston upon Thames, the front page of the hosts' match programme did not feature the name of their opponent, while the team list referred to them as Milton Keynes and their electronic scoreboard simply read 'MK'.
The EFL has now charged AFC Wimbledon under new regulations 3.4 and 3.5 which state "all clubs are required to behave towards one another with the 'utmost good faith' and not to 'unfairly criticise, disparage, belittle or discredit' any other club".
In response, the club released a statement which said: "The club has received notification from the EFL of charges relating to the Milton Keynes home game on Friday 22 September. The club is still deciding on its response to the charges and we will therefore be making no further comment on this matter for the time being."
AFC Wimbledon were formed in 2002 by Wimbledon FC supporters who were upset by the Football Association's decision to allow their club to move to Milton Keynes, and the strained relationship between AFC and MK Dons continues to this day.