The 25-year-old finally penned a new five-year deal on Friday - worth a reported £250,000 per week to the England striker - after initially citing United's lack of ambition as his reason for wanting to leave Old Trafford.
And speaking after United's 2-1 win over Stoke in the Premier League on Sunday, Ferguson spoke about how he had to draw on all his managerial experience to convince the former Everton prodigy to produce a dramatic U-turn and re-sign.
"It’s always tough at United. There are always issues to deal with," Ferguson said in The Mirror.
"I have experienced a lot of things that do happen and there have been times in the past when I have gone down the same road.
"When your top players come towards the end of their contracts, you have to do something to get them a new one. They’re all the same.
"You have to deal with agents of this world today, which is difficult. The players are no problem. There’s no problem with players. Some agents are difficult."
Rooney sought assurances over the direction of the club following the high-profile departures of Cristiano Ronaldo to Real Madrid and Carlos Tevez to neighbours Manchester City last year.
But after Ferguson and chief executive David Gill raised the issue with the Glazers, the American's are believed to have sanctioned a transfer kitty of around £50 million, available for a massive United rebuild in the summer.
Although agents came in for the majority of Ferguson's flak, the Old Trafford supremo also took time to hit out at the symbiotic relationship they share with the media, which led to Rooney's two-month contract deadlock being leaked through the press.
"The modern trend with agents is that they are never criticised by journalists because that is their feeding foundation," he said.
"I don't think you can deny we got a lot of publicity that we didn't enjoy [last week], but you have to deal with these situations and I think we dealt with it very well."
By James Martini
