The Premier League side have already seen both Robin van Persie and Javier Hernandez miss spot-kicks this season and Ferguson said he was not expecting to see Nani take the penalty.
"To be honest with you, I have no idea why Nani took it," the United manager told reporters after the game.
"I think Nani just ran and grabbed the ball.
"I thought Robin should have taken it, to be honest with you. I think we will have to decide before the game, which is my fault, I should have done that.
"We missed so many chances in the second half, that was the worrying part.
"Missing the penalty just after half-time still keeps them in the game. If it goes 2-0 at that stage, it would have been very difficult for them to get back."
|AT THE DOUBLE?
|13/2||Robin van Persie is 13/2 to score two or more goals against Liverpool with Paddy Power|
Despite his frustrations on what was a difficult night for the Red Devils, Sir Alex was pleased by the ovation received by midfielder Darren Fletcher as he returned for his first game for nearly 10 months.
He said: "I think the support recognised what a tough time he's had for the last year.
"I think that was a mark of respect, they gave him a marvellous ovation.
"Being out of the game for a year, it took quite a few minutes to really get going. He did one or two good things, but he can only get better after tonight."
However, the Scot was pleased his side were able to pick up the win, thanks to a goal in the seventh minute from Michael Carrick.
"Obviously after the experience of last season, which was unusual for us, the result was the most important thing," he added.
"We're satisfied to get the result that got us three points and the result with Braga losing at home to Cluj, makes it an interesting second game against Cluj."