Goals by George Elokobi and Kevin Doyle condemned United to their first league defeat of the season and deprived them of a club-record 30th straight league match without defeat - a run stretching back to last April.
Leaders United are now four points clear of second-placed Arsenal who had earlier thrown away a 4-0 lead to draw 4-4 at Newcastle United in an astonishing game.
"We are disappointed, particularly after going in front so early in the game," Ferguson told MUTV.
"The result was caused by bad play at set-pieces. That is the nuts and bolts of it and we don't dispute that."
When Nani cut in from the right to smash United in front after three minutes it looked as though they were on course for the club record and a vice-like grip on top spot after 10-man Arsenal's second-half collapse at St James' Park.
But Wolves, struggling to avoid relegation, had other ideas and Cameroonian Elokobi headed his first league goal in English football after United were caught sleeping at a corner and Matt Jarvis was given time to deliver a perfect cross.
Five minutes before half-time Nenad Milijas's free-kick caused confusion in the United defence and Doyle applied the final touch to deflect the ball past goalkeeper Edwin van der Sar.
United, who have won just three times on the road in the league this season, struggled to find a way back and became desperate for an equaliser with Paul Scholes lucky to avoid punishment after trying to punch the ball into the net.
"It was a great start," added Ferguson, who lost defender Rio Ferdinand to a calf injury in the warm-up. "We made a lot of chances, particularly in the first-half.
"Nani had two great shots at the goalkeeper, Wayne Rooney had a good chance too, so we played a lot of good football in the first-half and made some great chances, but we were never at the races in the second-half.
"We had an incredible amount of possession. The pitch wasn't very good, but nevertheless we never really created anything."
While depriving United of beating the 29-game unbeaten run achieved by Ferguson's 1999 treble winners, defeat also cost them chance of equalling Arsenal's 2003-04 feat of going through an entire Premier League season undefeated.
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