Swindon have been fined £15,000 after a confrontation in the 67th minute of the game at the County Ground.
Millwall were made to pay £5,000.
"We just have to educate the players a bit more on that respect for the referee," Swindon sporting director Seamus Brady told BBC Wiltshire.
"We're trying to educate them a little bit and just let them know that we have had a couple of instances in the past and that's what we need to be careful about moving forward."
Swindon and Millwall have been fined by the Football Association after admitting to failing to ensure players conducted themselves in an orderly fashion in the 2-2 draw on 12 March.