The La Liga club, who lifted the competition last season, were beaten by second half goals from Jens Toornstra and Karim El Ahmadi in Rotterdam.
Emery said: “We were unbeaten but we knew Feyenoord had improved and they were strong. In the first half the team was well but we changed after the goal.
“We were denied a legal goal so it was even more difficult. Now being first does not depend on us. You can’t blame the attitude of the team, we have tried hard.
“It’s hard to get credibility if you lose. We need to keep working and players need to keep growing. Credibility is greater when victory comes.
“Some players are debuting in Europe and some are going to be getting more experience as they play, but it can’t be an excuse.”
The result clinches qualification for Feyenoord, who leapfrog Sevilla into first place. The Spanish club have eight points from their five group games so far and sit one point ahead of third placed HNK Rijeka.