The furore over Wayne Rooney's omission and the performance of referee Cuneyt Cakir at Old Trafford on Tuesday night has rather obscured a brutal truth, namely United allowed their winning position in the last-16 tie to be overturned in the space of just 13 minutes, from the moment Nani was sent off for a high challenge on Alvaro Arbeloa.
Some of the blame has been placed at Ferguson's door, for failing to react, in contrast to Jose Mourinho, whose introduction of Luka Modric within three minutes of Nani's exit proved to be a masterstroke.
Others feel United's experienced players should have taken more responsibility for the situation and not allowed Real to score quite so easily.
However, Ferguson feels the controversial decisions that cost United so dearly in 2004 and 2010 played on minds as the realisation dawned exactly the same thing was happening.
"We lost our composure for that 10-minute period," said Ferguson.
"We were all over the place. There was a sense of: "here we go again".
"You have to admire Madrid - it was a fantastic performance from them. But that 10-minute period was the killer."
Ferguson has plainly never forgotten an incorrectly disallowed Paul Scholes effort against Porto nine years ago which would have given United extra protection against the late goal that eventually knocked them out.
Six years later, Rafael was sent off as United looked to protect a winning position after a similarly superb start against Bayern Munich, and they were beaten by Arjen Robben's brilliant effort.
"That's three European Cups we've been knocked out of due to refereeing decisions," said Ferguson.
"We would have won two of them. I have absolutely no doubt about that."
It was that knowledge which prompted Ferguson to try and whip up the United support as Mourinho was signalling for Modric to get changed.
Questions of Ferguson's wisdom are fair given what subsequently happened, although the Scot insists he did the right thing.
"I was angry," he said. "There's nothing wrong with losing your temper for the right reasons.
"I mirrored what every person in that ground felt.
"Knowing the damage it was going to do to my players, I did the right thing."
Ferguson has still not got over Cayet's decision, having opted not to attend the mandatory post-match press conference immediately after the game for fear his temper might boil over.
The situation was not helped by the reactions of Alvaro Arbeloa to being caught, nor Real skipper Sergio Ramos, who raced across to demand the Turkish referee take action.
"Arbeloa wasn't that bad," said Ferguson. "He didn't stay down too long.
"Ramos was the one that maybe influenced the referee.
"A couple of their players did apologise (for the result) and Ronaldo was great. He came into the dressing room and sat with the players."
And, strangely, though the loss of skipper Iker Casillas was supposed to be a massive negative for Mourinho's team, Ferguson believed it actually worked to their advantage.
"Casillas wouldn't have saved the shots Diego Lopez did; going out to Danny Welbeck, going down at Robin van Persie's feet, coming out and whacking Nemanja Vidic in the head," said Ferguson.
"Casillas isn't that type of goalkeeper. Lopez saved them."
But whilst disappointment lingers, Ferguson accepts dwelling on the negative is futile.
With a 12-point lead in the Barclays Premier League, United are still well placed to pocket some silverware, and should they come through Sunday's FA Cup quarter-final with Chelsea, they would be only two victories away from potentially a fourth domestic double.
"We have a job to do on Sunday and I think we'll do that okay," said Ferguson.
"We've gone through this procedure many times.
"When you're at a club for a long time there are always damp moments and dark days.
"In general we recover very well and we'll do that again."