For the third consecutive match, United missed a penalty, Nani halting in his run-up to try and wrong foot goalkeeper Fernando Muslera before seeing his attempt easily saved.
After Robin van Persie's miss against Southampton and Javier Hernandez's failure from the penalty spot against Wigan in the weekend 4-0 victory, it was an embarrassing and potentially costly error by Nani.
Nani reacts after missing a penalty against Galatasary. Photo: AFP
United only led 1-0 at the time of his miss early in the second half and their Turkish opponents not only twice hit the woodwork but were also unlucky to fail with two strong penalty claims of their own.
"To be honest with you I have no idea," said Ferguson when asked why Nani had taken the kick. "I think Nani just ran and grabbed the ball.
"I thought Robin (van Persie) 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."
Michael Carrick's early goal was enough to earn United a winning start to their Champions League group campaign, a win which leaves Ferguson as the first manager to win a century of games in the competition.
And the England midfielder, who scored his first European goal in three years, attempted to make light of the surprising record of penalty misses.
"The manager will probably have something to say but each time we've missed one we've won the game," he said. "So hopefully next time we get one we'll put it away."
More importantly, after the humiliation of last season when United failed to reach the knock-out stages of the tournament, the win also hands the English club a solid platform upon which to advance in this year's cup.
"Obviously after the experience of last season which was unusual for us, the result was the most important thing," said Ferguson. "Also for our club, it's about more than that.
"It's about playing a brand of football we're recognised for and at times today we did play some excellent football.
"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."
One undoubted bright point for Ferguson was the return of Darren Fletcher, the Scotland international midfielder sidelined since November 2011 with a bowel disorder that had threatened to end his career.
Fletcher played the last 11 minutes as a substitute and received a standing ovation from the home crowd upon his return.
"I think the support recognised what a tough time he's had for the last year," said Ferguson. "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."
Galatasary coach Fatih Terim was impressed by his team's strong display but less so by the performance of German referee Wolfgang Stark, particularly in his failure to award the Turks a first minute penalty for an obvious trip by Nemanja Vidic on Umut Bulut.
"In the beginning there was a penalty and if the referee had whistled, maybe the result would have been different," said Terim.
"Normally, he should see that, the position he was in. At the Champions League level, a referee needs to see that but the German referee did not. It's so interesting that at Old Trafford he couldn't see this, normally he should see this."