The fracas occurred late in the first half following a tackle from Everton's James McCarthy on Morgan Amalfitano, with a large number of West Ham players confronting the Republic of Ireland international.
Both McCarthy and Winston Reid were booked by Clattenburg, which will mean the West Ham defender is suspended for Saturday's Barclays Premier League clash with Newcastle.
The FA's disciplinary action stated "both clubs failed to ensure their players conducted themselves in an orderly fashion", with a deadline of December 1 for a response to the charge.
Allardyce said: "I can't argue with it
We got so frustrated probably by the decision of the referee at the time.
"We lost our control a little bit
I don't condone what we did, but I can understand why the frustration crept in.
"We have to try to control ourselves better in those situations because we could have easily lost a player to a red card in that congregation of players based on the feeling of frustration that they felt at the time.
"Both sets of players were involved
We have to try to keep more control.
"To be fair to my players they don't often do that
Very rarely do they lose control, rarely have they done that sort of thing in my time here.
"While I will remind them about it, I don't think it will be a particular problem for us."
West Ham went on to lose the match 2-1, having fallen behind in the first half to a goal from Romelu Lukaku which looked offside.
While Allardyce does not condone his players losing their cool, the Hammers boss believes had the referee clamped down on some late challenges, the heat would have quickly been taken out of the flashpoint.
"I don't think it helped
Particularly the first one, if he gives a free-kick and deals with the situation, we could have got on with it
Because he didn't give a free-kick that spilled over into frustration," he said
"When you see your team-mate is, to your mind, unfairly treated, then you want to stick up for each other.
"Obviously, you don't want to extend it to the levels that we saw on Saturday."
West Ham host in-form Newcastle, one of Allardyce's former clubs, looking to get back to winning ways following what has been a fine start to the season before the international break.
"We have let ourselves slip in terms of points gained over the past three games, where we should have accumulated far more," said Allardyce, whose side are sixth.
"It is all right saying that you have deserved more, but in this game you make sure you get more, come off the field having produced the performance and result that the performance deserved.
"We didn't do that against Aston Villa and Everton."
Source : PA
Source: PA