The result leaves Ferguson's men needing a point from their trip to Basle next month to qualify for the last 16 - and their chances of winning the group looking slim.
The Scot, though, felt his side deserved more for their efforts.
"I think we did well," Ferguson said.
"It is hard when you lose a goal straight away in a match and it took us a bit of a while to get our rhythm going again, but once we did we played really well.
"We didn't deserve what happened tonight, but football can be like that.
"If we had had just a few minutes after we had scored the second goal I think we would have been okay, but it was too early to lose that second goal."