The Dons fell to a 2-1 second-round defeat by Raith Rovers after Glass made seven changes for the trip to Stark's Park.
With the likes of Christian Ramirez, Lewis Ferguson, Scott Brown and Ryan Hedges on the bench, Aberdeen dominated the first half and led through Jay Emmanuel-Thomas' wonderful strike.
But Raith got a lift inside three minutes of the restart when Ethon Varian netted following a set-piece. And Dario Zanatta bagged a 71st-minute winner with young full-back Jack Gurr culpable at both goals.
There was more misery for the Dons when Jonny Hayes left the playing area on a stretcher and substitute Hedges limped away on crutches after both suffered late injuries.
Glass, whose side face Qarabag in Azerbaijan on Thursday, said: "The changes aren't about trying to be clever or rotate the group.
"I think we saw in the first half a group of players on the pitch that was more than capable of winning that game. We didn't quite do enough to put the game away at half-time, but that's not an issue over the selection.
"You saw at the end with Jonny and Ryan getting injured just how quickly we can get stretched pretty thin by injuries and so we have to make changes to protect players.
"We've got two young boys at full-back who are doing well but one's just turned 18, the other is 21, they're both in their first full season, so you have to offer a level of protection for the players.
"Today is a massive disappointment, I can't put a positive spin on the game.
"We didn't start the second half particularly well and we conceded an early equaliser. The atmosphere then becomes a cup-tie atmosphere and we allowed them to dictate the play which we didn't in the first half.
"The reaction to that, to be a threat and go and dominate the game again, wasn't there and that's probably the biggest disappointment."
Rovers boss John McGlynn also admitted the equaliser was the turning point but had always been happy with the way his side were shaping up.
"Goals change games and it gives you a greater belief," he said.
"I felt we created the best two chances of the first half. The boy Jet couldn't have hit his goal any better but it came from very little. It was unstoppable, we had done nothing wrong and ended up 1-0 down.
"I will concede Aberdeen had a lot of the ball but I can't remember Jamie MacDonald making too many saves. Even when it went 2-1 and you think we are going to get the kitchen sink thrown at us, again Jamie MacDonald didn't have an awful lot to do.
"It's testament to everyone in the team making ourselves very hard to beat and causing one or two problems at the other end. We showed composure in the second half that we didn't show in the first half."