Ferguson's decision to field a virtual reserve side backfired when his second string outfit was outplayed by the Sky Blues.
Of the players who beat Chelsea 2-0 at home in the Premiership on Sunday, only Wes Brown and Michael Carrick featured - both as second-half substitutes.
The Reds were woefully weak upfront where young Chinese international Dong Fangzhou was almost an isolated figure in the first half.
Coventry's undoubted hero was pacy Maltese midfield man Mifsud. Nicknamed The Mosquito by Coventry assistant manager Tim Flowers, Misfud stung shoddy United for two goals and could have had four.
His first strike came in the 27th minute when United's young bloods were caught cold at the back.
Leon Best's ball in from the right looked to be too long for captain Michael Doyle as he raced across the United penalty area.
But right-back Phil Bardsley's reaction to the potential danger was too slow, enabling Doyle to knock in a low cross to the far post from the left side of the box which Misfud bundled in from close range at the far post.
Misfud could have had a second goal three minutes later.
Robbie Simpson crossed from the right and Misfud produced an audacious backflip ten yards out which beat United goalkeeper Tomasz Kuszczak only to hit the post.
Misfud again capitalised on errors in the United defence to fire his team 2-0 ahead after 70 minutes. A long ball out of defence sent Misfud racing away down the left.
He cut in and left United defender Gerard Pique for dead as he raced into the box, exchanging passes with Jay Tabb before firing home a fierce right-foot shot from ten yards.
Misfud should have had his hat-trick 12 minutes later. Doyle touched a free-kick to Stephen Hughes, whose thundering 25-yard shot was only parried by Kuszczak.
Misfud followed up with the easy job of tapping the ball in from six yards, but unbelievably he shot wide.
United's best of their few chances came seconds before Coventry's second goal when Dong produced a superb glancing header from Nani's left-wing cross, which was brilliantly tipped behind by Sky Blues goalkeeper Andy Marshall.