They eventually lost 3-1, meaning Arsenal had an uphill task on their hands during Thursday's second leg at the Emirates stadium.
That's because Maitland-Niles' goal should not have stood.
It's hardly surprising that Emery has maintained the shape that was fruitful against Manchester United as Arsenal require goals tonight against Rennes. "The offside was very clear, you don't need VAR to see it".
He has reason to complain, though.
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"This comeback was very hard, but I think the reaction was very good from every player", Emery told reporters.
"I said to the players today, I'm excited (about) this competition, but it's exciting not only for the possibility to go to the Champions League, but also because it's one title", he said.
"It was very clearly an injustice, it was a manifest error", Stéphan said.
Aubameyang opened the scoring five minutes in when poking home an Aaron Ramsey cross, coming after some good link-up play between the Welshman and Maitland-Niles down the right. "The second goal changed things enormously, even if they were better than us and deserved to qualify".
"We are going to think the same before every match". At the beginning of the match, we lost too many balls, due to their pressing, we had tension, we were not at home.