"I have not had a word with the referee yet but the the fourth official [Alan Wiley] tried to give me an explanation of sorts as I was questioning the amount of time added on even before the game finished," stated Hughes.
"His explanation did not sit comfortably with me. He said a minute plus had been added because of our celebration. We scored on 90 minutes, the board was already up for four minutes, so Mr Wiley said he was going to add that minute on.
"The amount of time from when we scored to when we kicked off was something like 45 seconds. He has got that wrong as well. It was 95 minutes, 26 seconds.
"Obviously, he has played too much time and we ended up playing 97 minutes. I just needed an explanation as to why so much time was needed. United were given a little more time than they should have been given to get the goal.
We're disappointed, we put in a hell of a shift today
Manchester City Mark Hughes
"Historically it has happened before. I was in teams here where we always had a little bit of benefit. I never felt it was an issue when we played here.
"But since I have left maybe I have changed my view on that. I am not going to question anyone's integrity but I do not know where has got seven minutes from.
"It would be nice to get an explanation but I don't think I will."
BBC's Match of the Day 2 programme showed that, by the letter of the law, referee Martin Atkinson should have blown his whistle one second before Owen's winning goal.
After the fourth official indicated four minutes of added time, 56 seconds passed between Bellamy's strike crossing the goal line and play restarting.
As well as taking goal celebrations into account, the officials were entitled to add 30 seconds for United's stoppage-time substitution, when Michael Carrick come on for Anderson.
Therefore, the total amount of time that should have been added was five minutes, 26 seconds and Owen struck on five minutes, 27 seconds.
Atkinson then did not blow the full-time whistle until 96 minutes and 58 seconds were on the clock and Hughes believes the pressure of the Old Trafford crowd may have played its part.
"We've done really well to come back three times against Manchester United at Old Trafford," he added. "It's a big stage here and that puts everyone under pressure, including the referees.
City's £120m summer spending spree, including the capture of Carlos Tevez from United, added extra spice to the fixture, as did United boss Sir Alex Ferguson's pre-season dismissal of his club's neighbours as "a small club with a small mentality".
The visitors came back to level the game three times before Owen's late winner and Hughes revealed he was proud of his team's efforts.
"We're disappointed, we put in a hell of a shift today," said Hughes. "Craig Bellamy scored two magnificent goals. He didn't deserve to be on the losing side."
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