Ferguson's concerns were justified as United slipped to a 1-0 defeat thanks to Burak Yilmaz's second-half header.
It cost the Red Devils their 100% record in this season's competition, and means they have now conceded the first goal an incredible 12 times in 17 matches in both the Premier League and Champions League.
However, with 18-year-old Nick Powell hitting the bar on his first start, and Phil Jones making his first appearance of the season after back and knee problems, there were obvious plus points as well.
"We worried about set-pieces and that was the area we suffered," said Ferguson.
"That was always going to be a problem considering the lack of experience and height.
"But otherwise it was a decent performance. Parts of the game were good and we handled the atmosphere."
Ferguson was critical of early challenges from Felipe Melo and Semih Kaya, both of which he felt warranted red cards.
Spanish referee Carlos Velasco Carballo opted to keep his cards in his pocket though, and Galatasaray took advantage, with Hamit Altintop twice coming close in addition to Yilmaz's fifth goal in the competition.
At least though, the damage is not as serious as 19 years ago, when United were sent crashing out of the competition.
The stadium is different as well, even if the incredible noise levels seem to be the same.
"It is a fantastic stadium and obviously an improvement from the old one," said Ferguson.
"There is not much difference in the atmosphere.
"The biggest change since then is that we have won the competition twice and we have qualified for the last 16 this year too."
Galatasaray will join them if they match Cluj's result at Old Trafford in a fortnight.
"We'll play a similar team against Cluj, that goes without saying," said Ferguson.
"We've qualified and there's no reason why we shouldn't use the squad."
Galatasaray coach Fatih Terim was understandably delighted at securing such a notable triumph.
"We deserved this victory," he said.
"We dominated the game and in the end found the goal that we needed. When you play against a team like Manchester United, you cannot go slowly. You have to be enthusiastic and wise.
"I am fortunate my players were able to be both things this evening [Tuesday]."