Federico Macheda's late strike was too little too late for Paul McGuinness' young Reds, who went down 2-1 to Crewe at Carrington on Saturday.
The Reds were left frustrated by a determined display from the visitors, whose two decisive goals on 53 and 68 minutes left United too much to do to bridge the gap.
Good chances fell to Nicky Ajose and Chris Curran in the first half, but neither could convert. Had those chances been taken, the tale of this clash could have been very different.
Crewe took the lead with a breakaway attack on 53 minutes and, before McGuinness' subsequent substitutes Macheda and Evandro Brandao had a chance to influence the game, the Railwaymen snatched a second on the counter.
A typically clinical finish from Macheda in the 89th minute proved little more than a consolation for the Reds.
There are undoubtedly lessons United's youngsters will learn from this defeat, one being just how difficult Group C of the Academy Premier League can be if you're not on top of your game - Crewe had start the day bottom of the table.
The defeat brings United's unbeaten start to the season to an end, and McGuinness will hope for the right reaction in Saturday's away visit to Wolves.
United: Devlin; Strickland, Brown, Wootton, Gill; Curran, Norwood, Tunnicliffe, Stewart (Brandao 64); Ajose, Bryan (Macheda 64).
Sub not used: Woods (GK)