Ferguson's men were missing Wayne Rooney because of a virus and they lost ground on Premier League leaders Chelsea when Nani missed an 87th-minute penalty that would have secured a 3-1 lead - a spot kick the United boss thought Ryan Giggs should have taken.
Nani's effort was well saved by David Stockdale and in the final minute Brede Hangeland, whose own goal had nudged United ahead, nodded home the equaliser to earn Mark Hughes' side a share of ther spoils.
"When you get the opportunity to seal the game with that penalty you should be taking it,'' Ferguson told MUTV. "It was a missed opportunity and it galvanised them, got the crowd up and they scored the equaliser in the end.
"I thought Ryan should have taken it. In the last game we played against Tottenham at home Ryan scored two penalty kicks and Nani was on the pitch the same day. Maybe Ryan should have taken it.
"When we got that second goal I thought 'we've escaped here'. But to miss a penalty kick to make it 3-1, you're throwing two points away there I'm afraid.
"You don't want to be dropping silly points and we dropped silly points today. We can't escape that. There was an opportunity to go 3-1 ahead with three minutes left and we didn't take it.''
Ferguson's frustration at failing to join Chelsea at the top of the table was tempered by the admission Fulham deserved a point from an enthralling contest. An ominous start from United saw Paul Scholes fire a powerful 25-yard drive in the 11 minute only for Simon Davies to equalise in emphatic fashion during a second half controlled by the Cottagers.
"In fairness to Fulham they were the better team in the second half. I don't think we deserved to be in front at 2-1,'' Ferguson said. "They caused us a lot of problem, particularly Bobby Zamora who was very good for them. We can't complain in terms of the run of the game.''
Ferguson added: "We've seen that before from Paul - he's done that so many times. Once again it was an outstanding performance from him. It's just disappointing we didn't ram home the advantage.''
The United boss confirmed that Rooney, who has gone 13 games for club and country since his last competitive goal, was ruled out through illness. "Wayne has a virus," Ferguson said. "The problem is he turned up yesterday with it and he had no chance in 24 hours.
"If it had been a Thursday or Friday we may have been able to patch him up. Sometimes these viruses are 24-hour things and that could have been the case but there was no attempt to see if he could recover from this.''
Fulham had Stockdale's reflexes to thank for keeping them in contention but boss Mark Hughes was wary of lavishing praise on the 24-year-old. Arsenal target Mark Schwarzer, who has handed in a transfer request, failed to recover from his back injury so Stockdale continued between the sticks.
"Stockdale has done very well, he's a good young keeper,'' Hughes said. "We're pleased with what he's producing at the moment but it's always difficult for young keepers. They get by initially on enthusiasm, but can they keep it up over time? We've got to be careful with him.''