The Premier League champions conceded in the 87th minute when Juan Mata's effort was deflected in by Phil Jones after a possible foul committed on Wayne Rooney whilst Rafael was sent off for an incident involving David Luiz in the final minute of regular time.
Despite the controversial incidents, Ferguson felt his side were simply not good enough on the day to take all three points.
"I don't think Wayne (Rooney) was fouled (prior to the goal), but the referee was giving us nothing anyway," he told Sky Sports.
"It was a bit lucky, the goal, it was deflected off Phil Jones. It was so late in the game there is not a lot you can do about that."
Of the red card he added: "Unfortunately it was controversial, it is like that a lot of times when you play against Chelsea.
"But we can't complain, we didn't play well enough."