After the game Ferguson was in no doubt as to the defensive display from his side that could have cost them a vital victory in the title race.
"I don't know what to make of it, the first half the defending was the worst this season, absolutely no doubt about that," he said. "Nobody competed for the crosses, in fairness Reading have a great delivery of the ball - the boy (Nicky) Shorey whips them in, fantastic crosses but we should be doing better than that. It was terrible."
United have now won seven league games from losing positions and Ferguson was pleased with his attacking players during the opening 45 minutes.
He said: "We have the players that can rescue us and today again Waz (Wayne Rooney) in the first half was fantastic, he and Robin (van Persie) and Ashley Young were a real threat to them, they couldn't control them.
"They were terrific in the first half, Ashley was right back to form and gave them a real hard time of it - Wayne made a great pass for Robin's goal, terrific pass.
"There are a lot of plus points in the sense that they never gave in and kept going and in the second half showed a great determination to get over the line and that is what it was about today, getting over the line."
Reading boss Brian McDermott was pleased with the performance from his players and was philosophical about the bittersweet defeat to the league leaders.
"I thought some of the football was terrific - I thought we were going to go on and win the game but they have got massive quality in the team and we know that," he said. "I look at that today and I remember where we were three years ago, we were just coming up to a game with Plymouth and we got beat 4-1 and it could have been about 10.
"We were staring Division 1 (League One) in the face and where we are now, three years later, is a phenomenal achievement for the club - I'm stood in line next to Sir Alex Ferguson playing Manchester United and we are 3-2 up."
Source: PA
Source: PA