Ferguson claims it is "hard to keep your faith" in football after decisions like Nani's red card on Tuesday - but referee Cuneyt Cakir still insists he made the right call.
He can also look back to a disallowed Paul Scholes goal against Porto in 2004 and Rafael's red card against Bayern Munich in 2010 for other examples of when refereeing decisions have gone against his side, and he admits that is quite dispiriting.
"It's hard to keep your faith when you see what's happened in the last few years," said Ferguson.
"It's the third time we've been knocked out by a referee's decision and it's not easy to take.
"I was concerned before the game. I said that to my staff. I had a big worry about it. But it's gone now. We have to get on with it."