Replays clearly showed the Scottish international had been brought down in the CSKA penalty area.
The United boss described it as "the worst decision I have seen in my life" and was mindful that Fletcher missed last season's Champions League final after what appeared to be a similar mistake.
McLeish has sympathy for Fletcher's plight and Ferguson's stance on being allowed to contest such decisions.
The former Scotland boss said: "This (appealing against yellow cards) is something that was brought up at a UEFA meeting a couple of years ago I was at with a lot of the top coaches.
"That was a topic back then because there are a lot of injustices. The Darren Fletcher situation was ridiculous. There are so many things that referees miss.
"I know we can't re-referee games but there are real miscarriages of justice."
Meanwhile, McLeish is adamant veteran striker Kevin Phillips still has an important role to play at Blues after being linked with a move to Middlesbrough.
Phillips has had to be content with a bit-part role this season behind the likes of Christian Benitez, Garry O'Connor and Cameron Jerome.
McLeish, whose side visit Liverpool on Monday, said: "We don't have any plans to get Kevin out of the door.
"Kevin is still sprightly on the training ground, he is still worth something to our squad. His contribution to the Bolton game recently was good.
"I know he wants to play every week and feels at 36 he is capable of doing that so I understand his frustration."