Shortly before half-time in the game at Goodison Park - which West Ham lost 2-1 - a heavy challenge by Kevin Mirallas on Morgan Amalfitano sparked an angry reaction from the West Ham players.
A bout of pushing and shoving broke out, before tempers were eventually calmed.
On Wednesday, the FA confirmed that both clubs had been charged with failing to control their players, something which Allardyce readily accepts.
"I can't argue with it," he said in a press conference on Thursday.
"We got so frustrated by some of the decisions that we lost control a little bit. I don't condone what we did but I can understand the players' frustrations.
"We need control ourselves better because we could have lost a player to a red card. Both sets of players were involved.
"To be fair to my players they very rarely do that. I'll remind them of their responsibilities but I don't think it's a particular problem for us."
Andy Carroll made his first start of the season at Everton after recovering from an ankle injury, and with former club Newcastle United visiting Upton Park on Saturday, Allardyce is glad to see the return of the 25-year-old.
"We're happy to see every player who comes back from injury," he said. "It's a big boost to have a player like Andy back after such a long time.
"He did well considering he wasn't expected to play the 90 minutes. He's in the process of completing a pre-season before we see the best of him.
"It'll take a way until he's back to full fitness and when he is that's when we'll see the best of him."
