"Maybe Wayne's representatives have taken a position to negotiate a new contract but maybe they've miscalculated," he said.
Related ArticlesTevez: we will win everything with RooneyDeath threats sprayed onto Rooney posterEvra puts the boot into disloyal RooneyRooney's house besieged by angry Man Utd fansRooney offered olive branch by UnitedRooney v Ferguson"The position they're in makes it very difficult for Wayne to come back from.
"Whether or not that was the intention initially, they have overplayed their position.
"I hope Wayne stays at Manchester United. He's at the right club at this moment in time - he's got good people around him.
"Sometimes the grass isn't always greener. Sometimes agents can be a really positive influence, but sometimes they can make your job harder.
"We all have to deal with player power. The nearer a player gets to the end of his contract, the more the power shifts to him and his representatives."
Hughes believes Sir Alex Ferguson's handling of the episode highlights his adaptability as a manager.
"Sir Alex understands that football changes very quickly and he's been able to change with it," said Hughes.
"His approach to similar situations in the past would have been different. That shows what a good manager he is."
Stoke manager Tony Pulis has backed Ferguson to keep attracting big-name players to United and continue his "dynasty" at the club without Rooney.
Pulis said: "I think they are managed by probably the greatest manager that has ever managed in British football, and Sir Alex will have players up his sleeve to come in.
"He has kept that dynasty for many years, and he will keep it going. He is a top, top manager and I think he will be more determined now than ever to get this right again.
"One individual won't stop them from being a great club. He (Ferguson) is too good to let it slip and he will be doubly determined now to get the next great player, bring them in and push the club forward.
"The football club is in good nick and when you have got a man like him in charge, you don't have to worry too much."
Although Rooney's comments have caused shockwaves, Pulis - whose team host United on Sunday in the Barclays Premier League - insists he is not surprised to see the 24-year-old seek out a move, given the emergence of a "massive player" in the transfer market like Manchester City.
"You've only got to look at what has happened at other clubs. Manchester City have come into the game now, they are a big player, a massive player.
"When Chelsea got taken over by Roman Abramovich, there were loads of players going to Chelsea that you would never have imagined going there.
"It happens, and the big shock for everybody is just because it's Wayne and because of which club he is at.
"This has been going for years - I don't think this is the first case where a player has come in and said he wants to move for whatever reason. Money is power, it's always been the same.
"Manchester City were taken over and they have signed players that other clubs didn't want to release - look at the (Joleon) Lescott situation. Everton did not want to release Lescott."