Marsh-Brown, 19, had already been red-carded for a two-footed tackle on midfielder Josh Walker during the game.
After reviewing video footage of the incident which appears to show Marsh-Brown punching Thompson afterwards, the Latics player has been summoned to a disciplinary hearing at Wembley on Wednesday.
Marsh-Brown starts a three-match suspension this weekend following the initial red card, and faces the prospect of the 19-year-old having the length of the ban increased.