The Spaniard blamed poor finishing for the defeat, which was their second of the new season.
The Gunners went 2-0 down before fighting back to 2-2 before half time thanks to goals from Henrikh Mkhitaryan and Alex Iwobi.
But Mkhitaryan, Mesut Ozil and Pierre-Emerick Aubameyang were all guilty of missing clear chances to score.
And it proved costly as Eden Hazard came off the bench to set up Marcos Alonso’s late winner.
Emery told BT Sport, “We want to win. This is always the way but it is clear that defensively we suffered three goals but also we had chances to do more goals.
“I think the result is 3-2 but we also think we did chances to do more score.
“In the first half we are creating chances to score, and for that I am happy, I am in the match thinking we are well on the pitch.
“But also they had options, chances to score and effectivity (sic) is the difference.
“Our reaction is good, we had chances to go 2-2 and we deserved to do more at half-time.
“The half-time is good for us and the second half is we need to continue this control, but I think the second half we don’t push and keep possession like we did in the first half, and in our moments, our chances, we didn’t do, and they did.
“That is why the results is 3-2. But it is one process. In the second half we played with two midfielders, 19 and 21 years old.
“They improve and are continuing. I am happy without the result.”