Fourteen supporters have been charged with a variety of offences following the Elland Road encounter, with fans of both sides aiming insults at each other during the Premier League champions' 3-0 Carling Cup third-round triumph.
Visiting fans held up a banner depicting 'Istanbul' a reference to the two Leeds United fans who were killed in Turkey 11 years ago, with their home counterparts responding with taunts about the 1958 Munich air crash.
However, Ferguson revealed the problems had begun much earlier, as his team prepared for the game in their city centre hotel.
And whilst he has always viewed Liverpool as the real derby for his team, the animosity around Leeds clashes is far worse.
"Historically, it has been there for a long time," he said. "I have always said Liverpool-Manchester United games are fierce in many aspects.
"Sometimes supporters can play a bad part in that particular game. But it never reaches the levels of Leeds United. Never.
"It was frightening at our hotel. We had seven police vans round the hotel protecting the team.
"I don't know why it is like that. I don't understand it. But it is there and it is not nice."
On Friday, QPR manager Neil Warnock joined the chorus of people condemning those involved in the trouble at Elland Road and believes it was a sad night for English football.
"What are you going to do? Are you going to ban everybody?" he said.
"I mean there were thousands, it wasn't just one or two the other night. It is horrible.
"I obviously get called names at certain local derbies that I've been involved in and I try and smile at the crowd without actually bringing it on.
"But I think the other night it went beyond that. I thought it was very sad the other night.
"The Munich and the Istanbul chants, I don't think English football came out of that with any credit.
"I thought it was disappointing because of the families involved. You've got to respect people like that.
"Football is a game and I hate to see things like that because it takes away from what we are all in it for.
"It doesn't divide opinion because I don't think there's anyone who feels people were right to do what they did the other night.
"Why they do it, I just don't know."