Paul McGuinness will still take heart from the makeshift team's performance with most of the Under-18s away in Italy taking part in the Memorial Claudio Sassi tournament.
At least Reece Brown and Scott Wootton were drafted in to bolster the defence but there was a debut for Josh Harrop and a first start for Kenji Gorre.
The Toffees were the better side in the first half and deserved their lead at the interval which arrived around the 15-minute mark. Although Conor Devlin will feel he should have done better with it, the keeper made some smart stops to keep United in the game before being beaten again after 57 minutes.
Otis Khan, Ben Barber and Ryan Shields all came on for their debuts in the second period and there was a reward for a dogged performance when James Wilson's low left-footed strike gave McGuinness' youngsters hope late on.
The 15-year-old England schoolboy will be delighted to get off the mark at this level after almost breaking the deadlock shortly beforehand. United finished the game strongly, and were competitive throughout, as Wootton was thrown into attack in a desperate bid to force an equaliser.
United: Devlin; R.Brown, Rowley, Wootton, Wilkinson; Ekangamene, Leao (Khan 55), Harrop (Shields 83), Rudge, Gorre (Barber 77); Wilson. Unused subs: Sutherland, Ioannou.