The charge relates to an incident where United players confronted referee Craig Pawson after he had initially allowed a goal by Liverpool's Roberto Firmino.
The video assistant referee ruled out the goal for a foul by Virgil van Dijk on keeper David de Gea in the build-up.
United have until Thursday to respond.
The incident, which happened in the 26th minute as Liverpool led 1-0, saw De Gea booked for his protests to Pawson.