While shocked by the penalty conceded by Tyrone Mings, Emery conceded Brugge did enough to earn the three points.
"I don’t know if it was intensity," he said. "It was a mistake. The first half we played like we were planning. We had two chances, we had some corners and didn’t concede a corner from them. We didn’t let them play in transition, we didn’t make mistakes. The second half after the goal … it’s Europe. I have played in Europe for 16 years in a row.
"This situation I had before, not a mistake like that, but I had before. I know the difficulties we are going to face. We have experiences and I told them that the most important thing is the experiences we are having.
"Last year we lost to Warsaw, Zrinjski we drew, we deserved to lose at Ajax and we lost to Lille. It is difficult and here it is not strange. You watched the match and them playing, they finished exhausted. It was not intensity, it was that the match changed completely after our mistake."
He added: "We played the first half more or less like we planned and we controlled the game. We didn’t concede a lot but they were in our box to or three times being dangerous.
"The control was for us and we created some chances and we knew before the match to win we had to be patient. We had to avoid mistakes and we made a big mistake in the second half, that was the key.
"After their goal they were defending very well and focused on their game plan. We needed to push more, but in transitions they were dangerous. We didn’t have good chances in he second half. In the end we lost and I think the result is fair."