Villa struggled in the first-leg of their round 16 tie at the Amsterdam Arena.
Emery later admitted: "It is always difficult to play away in Europe, here you see the atmosphere they have.
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"It was a very high-level match, we are taking experiences in Europe and we can feel favourites but it's very difficult and if you're showing in other matches in Europa League or the Europa Conference League you can see some big surprises.
"I'm happy. We didn't play well, we didn't control the game like we prepared and like we usually do but I accept that as well."