Manchester United captain Wayne Rooney has denied asking to leave Old Trafford during Sir Alex Ferguson's final season in charge, but has admitted that he and other members of the squad had major problems with the Scottish manager during the 2012/13 campaign.

Rooney previously asked to leave United in October 2010, before being convinced to re-sign on much-improved terms. Ferguson then left the England international out of the squad for his final game at Old Trafford, a 2-1 win over Swansea, as he was again angling for a move away.

"I don't think Wayne was keen to play, simply because he's asked for a transfer," the Scot said then to Sky Sports. "I think he wants to think things through in his own mind. I think that's a good idea. We're not going to let him go. I think he's maybe a bit frustrated at being taken off once or twice in the past few weeks."

Rooney, however, has denied the version of events put forward by his former manager, saying he never wanted to leave the club – but admitting he was disappointed at being left out of the line-up and played out of position that season.

"It wasn't just me who had a fall out with him," Rooney said as part of The Man Behind The Goals, a documentary piece to be shown on BBC One. "I don't know what happened or why that came out that way. I went in to see him and just said if you're not going to play me it might be better if I moved on – then all of a sudden it's all over the press I put in a transfer request, which I never did."

Despite his problems with the Scot, Rooney still describes Ferguson as "the best manager of all-time", admitting he was the main reason behind his move from Everton in 2004.

"For him to be interested in me and want me to come and play under him, there was nowhere else I was going to go," Rooney admitted.