The Dons went down 2-0 in Gothenburg but made it safely through to a third-round meeting with Icelandic side Breidalblik thanks to a dominating 5-1 first-leg victory at Pittodrie last week.
Second-half goals from Martin Olsson and Leo Bengtsson made things a little nervy but a red card for Patrik Walemark, who was booked twice in quick succesion, undermined the hosts' comeback.
Referee Adam Farkas was a busy man in the last 22 minutes, flashing no fewer than ten yellow cards and drawing the ire of both teams.
Glass was unimpressed with what he saw from the Hungarian, including his failure to punish Hacken for an aerial challenge which forced off Jay Emmanuel-Thomas with a head injury.
The Aberdeen boss said: “Jay took a crack on the face when the opponent was nowhere near the ball so it was strange there wasn’t a free kick given for it when you see Jay’s eye.
“Declan got booked for kicking the ball away because you’re delaying the restart, but there was a sub being made at the time. So he didn’t delay it.
“I don’t think the officials helped us tonight but it is what it is. You come up against that in Europe and if we have that problem for a long time then it’s a good one.”
Despite the defeat, Glass was still happy with his side’s performance as they wasted a few chances to make things a little easier on themselves.
He added: “Obviously we are not happy to get beat at any time, but the performance and the result last week gave a very good team the chance to play carefree against us.
“You saw tonight how good Hacken are and it showed exactly how good a result it was from us last week. I was really pleased with the way we closed the game out.
“Hacken started well but other than that initial bit, there wasn’t too many times I thought they should have scored. Whereas at the other end I felt we had three or four good chances and if we had been sharper in the final third we would have.”