England international Rooney appeared set to leave Old Trafford when Ferguson revealed early last week that the 25-year-old had intimated he would not be signing a new contract.
However, on Friday, Rooney performed a remarkable U-turn by agreeing a bumper new deal which ties him to the Premier League giants until 2015.
The role of Rooney's representatives in the issue has been questioned and Ferguson believes the agents may now wield too much power.
When asked if privately he always thought Rooney would stay, the United boss told Sky Sports: "Not necessarily no, because although you know the player you don't know his agent.
"Agents live in their pockets nowadays and for some reason they have an influence on the players which I think is a big change in the game as far as I'm concerned."
However, Ferguson revealed he was not surprised by how the situation unfolded, commenting: "I don't think it's any different from any important times when important players are running around towards the end of their contract.
"It's a fact of life today we've got with agents and the type of agents we've got nowadays. You expect all these things.
"I wasn't surprised to be honest with you. You have to manage round that and I think we've done it well."
Prior to signing his new deal, Rooney had issued a statement which questioned United's ambitions for the future, but Ferguson has stressed he is building a new team to challenge for honours.
He continued: "At the end of the day, I'm in charge of that and if anyone has any doubts about Alex Ferguson's ambition there's something wrong there.
"I've been here for 24 years and the longer I'm here the more expectation there is regarding me and I'm well aware that if we're not doing well there's a tremendous amount of criticism too, as well as credit when you're winning things.
"We build teams, we've been doing it for years now. We know how to build teams and we've always had a foundation of young players who develop at the club who replace the older players as they go along and in three years' time you'll see a different United."