Wimbledon FC, who won the FA Cup in 1988, were known as 'The Dons'.
The EFL have asked AFC Wimbledon to provide relevant information about Friday's third tier match.
Wimbledon referred to MK Dons as Milton Keynes in their match coverage and excluded them from their matchday programme cover, despite giving the EFL assurances that the game would be treated the same as any other home fixture.
"The failure to recognise MK Dons in the correct manner causes reputational issues for the EFL as well as creating the potential for unrest amongst MK Dons supporters and, as such, is of concern for the EFL," the EFL said in a statement.
If Wimbledon are charged with breaching the regulations after the investigation, the case will be passed on to the league's Disciplinary Commission.
(Reporting by Aditi Prakash in Bengaluru; Editing by Toby Davis)
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