Fulham put a patched-up United to the sword on Saturday, winning 3-0 at Craven Cottage as the champions struggled to cope without centre backs Rio Ferdinand, Nemanja Vidic, John O'Shea and Jonny Evans.
United, who have already lost five league games this season, are also without the experienced Wes Brown and Gary Neville which meant midfielder Michael Carrick was again used as a makeshift centre-half on Saturday.
Young Belgian defender Richie De Laet also made only his sixth appearance at senior level.
"I hope that defeat doesn't prove too damaging," Ferguson told the club's television channel.
"In other words I hope it doesn't cost us the league.
"There was a fragility at the back today but we couldn't do anything about that. I have sympathy for my players because it's difficult for midfielders to play as centre-backs and De Laet's only 20 so he's not got the experience you need for these type of matches.
"The players are feeling a little bit sorry for themselves at the moment because of the situation they find themselves in," said Ferguson.
"But I think it's obvious if we get our defenders back we'll be okay. We need to get them back to give us a proper chance of challenging for the league."
United, who have not lost five matches at this stage of a season since 2001/02 when they finished third, also received sympathy from Fulham manager Roy Hodgson.
"We were playing a Manchester United side suffering very badly from injuries but we can't do much more I suppose than play as well as we can play and get the best result we can get," he told the BBC.
"I have got a lot of sympathy for Alex at the moment because it is not easy when you are missing a whole back four."
