Danny Murphy, Damian Duff and Bobby Zamora came up with the goals that did the damage against a United side that has seven recognised defenders out through injury.
A down Alex Ferguson told MUTV: "The way the league is at the moment I hope today is not too damaging. I hope it doesn't cost us the league.
"We'll have to get our defenders back to give us a proper chance of going for the league, there's no question of that. But if we get them back we'll be back in it.
"The quicker they're back the better. They're doing their best. The medical team and physios are working overtime to get them back.
"There's no light at the end of the tunnel at the moment, that's for sure."
Ferguson continued: "There was a fragility at the back and we couldn't do anything about that.
"You have to have sympathy for the players in that respect.
"It's difficult to play midfielders at centre back and Ritchie de Laet is only 21 years of age. He's not got the experience yet needed for these type of matches.
"Of course it was a terribly soft goal for the first one and that gave them the platform to build on.
"The goal after half-time took care of us. It was a poor decision by the referee for the third goal.
"We couldn't get behind Fulham at all and their defence is very well organised and it was a difficult day for us.
"The first goal was important for them but it was a bad one for us. It was an uphill fight after that.
"To concede 20 seconds into the second-half killed the game. We didn't anticipate that.
"The players are maybe feeling a bit sorry for themselves at the moment because of the situation they're in.
"But the quality of the football wasn't as good as it normally is.
"The fragile nature of the players at the back, with midfielders playing in defence, has left them feeling sorry for themselves a bit."