"There are lot of things I think he's done wrong".
The 53 year-old has struggled to become a favourite with the fans at the Emirates after failing to meet promises.
"He grew up in the academy and we need to give young players the opportunity to stay with us, work every day and play matches like today", Emery added.
The Spaniard named a strong starting line-up featuring Alexandre Lacazette, Pierre-Emerick Aubameyang and Aaron Ramsey, but they were largely eclipsed as Atletico beat the Gunners 3-1 on penalties after the teams were tied 1-1 after 90 minutes.
The Czech shot-stopper, who is in a similar situation with one year remaining on his own contract, was asked about Ramsey's prospects and said: "That's a private matter for the club and the player".
Jose Mourinho sends clear Man United message to Anthony Martial
And now the commanding centre-back is on United's summer shortlist as Jose Mourinho looks to bolster his defensive options.
In a statement Arsenal said: "We are aware of the speculation surrounding our chief executive Ivan Gazidis". I want him to stay with us, to work with us, to give the team big performances with his quality.
On Wednesday, he said Emery had convinced Arsenal's young guns that they can shine, and yesterday it seemed he took that to heart. "I don't know what he's going to do because I only speak with him about the Arsenal project".
Atleti's Luciano Vietto broke the deadlock at National Stadium with a headed goal from an Angel Correa cross four minutes before half-time, but the lead lasted just two second-half minutes thanks to a superb Emile Smith Rowe effort for the Gunners.
Obviously we'll continue to be without the likes of Lucas Torreira, Granit Xhaka, Stephan Lichtsteiner and Danny Welbeck as they are still on holiday following their World Cup exploits.