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Hargreaves joined United from Bayern Munich in 2007, winning the Premier League and Champions League double in 2008.
Injury plagued his time at Old Trafford however and he made just four more league appearances after his debut campaign.
The former England international left at the end of his contract in 2011 and Ferguson knew there was something off.
Per Pundit Arena he penned in his second autobiography: "I would say to him, 'How are you this morning?' 'Great, boss,' he would reply. 'But I think I'll do something on my own. I'm feeling it a bit.'
"When I signed him, there was something about him I didn't like. The thing every good leader should have is an instinct. Mine said to me: 'I don't fancy this.'
"When he came over to Old Trafford for the medical, I still had some indefinable doubt. He was very hail-fellow-well-met. Almost too nice."
Hargreaves was an important player in his first season at United and started the Champions League final against Chelsea.
He also scored a vital free-kick in a 2-1 victory over Arsenal which all but sealed the title.
Ferguson spoke highly of Hargreaves' ability as a midfielder while making note of his versatility.
"He could play right-back, wide right or central midfield.
"I played him wide right in the 2008 final against Chelsea, and when we started to struggle against their midfield three, I put him in the middle of the park with Rooney wide right and it worked. He had definite value.
"But it was all lost in the fog of his lack of games. Yet, Hargreaves was fantastic for England at the 2006 World Cup, plugging gaps, racing to the ball."
Overall though, it's a transfer considered a disappointment.
Ferguson continued: "I look back less fondly on our move for Owen Hargreaves, who was phenomenal in the summer of 2006 and was just the type of player we needed to fill the gap left by [Roy] Keane.
"We started to put together a bid for him. But I studied his playing record and felt a tinge of doubt. I didn't feel a strong vibe about him.
"David Gill worked hard on the deal with Bayern. I met Owen's agent at the World Cup final in Berlin. Nice man, a lawyer. I told him we could develop Hargreaves at United. It turned out to be a disaster.
"Owen had no confidence in himself whatsoever. He didn't show nearly enough determination to overcome his physical difficulties, for my liking. I saw him opt for the easy choice too often in terms of training. He was one of the most disappointing signings of my career."