Hughes wants an explanation to why Michael Owen was allowed to score in the 97th minute of the 4-3 win to United.
The fourth official indicated just four extra minutes.
“We need an explanation because I don’t know why the referee has added that amount of time on,” said Hughes.
“We just feel a little bit aggrieved that they were given that time.”
“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,” Hughes continued.
“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.
“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.”