With Jo, Benjani and Darius Vassell all absent, Hughes decided to go with a strike partnership of teenagers Daniel Sturridge and Felipe Caicedo.
However it was Danny Olsen who scored the vital goal after 16 minutes following a mistake by home skipper Richard Dunne.
It leaves City facing an uphill task in the second leg of this second qualifying round in a fortnight but Hughes feels they will be better equipped as they will be into their season.
He said: "I felt this was the most difficult draw out of the teams we could have met and so it proved.
"We did not help ourselves, certainly in the first half, when they scored the winning goal. From that point of view it was very difficult.
"We needed a spark to help us unlock the door but we did not have that.
"However the second leg comes round we will have more games under our belt. Hopefully we will make a better fist of it than we did tonight."
Hughes claimed he did not see Michael Johnson throwing an elbow on Gheorghe Florescu late on in the game.
The incident was caught on camera but the City manager said: "I haven't seen it so I can't comment."