Richard Chaplow put Southampton ahead on the stroke of half-time but after the second-half introduction of Nani and Ryan Giggs, Michael Owen levelled before Javier Hernandez hit the winner.
"Sometimes we make it difficult for ourselves but, in fairness, I maybe meddled with the system somewhat," Ferguson told MUTV.
"We tried a diamond in the middle of the pitch and, of course, Manchester United are used to playing with width all the time and I think that was a problem for us.
"It wasn't working at all," he added. "We had some possession of the ball but we never really threatened. We had two or three shots from the edge of the box.
"It was a nothing first half, really, and the goal, if anything, made us play. (Southampton) scoring the goal right on half-time motivated us a bit to do better."
Source: PA
Source: PA