Scholes, who is assisting coach Nicky Butt, was frustrated by the Reds’ first-half display against the German side, who went into the break two goals and a man up after Liam Grimshaw’s dismissal.
United grabbed an instant lifeline in the second half when James Wilson blasted home a penalty after being brought down in the box by keeper Oliver Schnitzler, who was subsequently sent off.
And thereafter the young Reds created several presentable opportunities to equalise, twice being thwarted by wonder-saves from substitute stopper Raoul Leuchter, before Leverkusen wrapped the game up with a sucker-punch third late on.
Nevertheless, Scholes saw enough to be encouraged that United can still qualify for the last 16 of the competition by beating Shakhtar Donetsk at home in the final game of Group A next month.
"We paid for a poor first-half display," Scholes told MUTV. "We didn’t really create anything, let two sloppy goals in and it wasn’t until the second half that we really started to play.
"With the amount of play we did have in the second half, we’d have at least hoped for a draw but unfortunately they scored on the break late on at a time when we had to throw