Hughes, the Fulham manager, suggests a game of brinkmanship over a new deal has backfired on Rooney but hopes he finds a way to stay at Old Trafford.
"Maybe Wayne's representatives have taken a position to negotiate a new contract but maybe they've miscalculated," he said.
"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."