The Gunners secured qualification for the last 32 with a 0-0 draw against Sporting Lisbon at the Emirates, in a game where Emery fielded a mixed-strength team including Emile Smith Rowe and Carl Jenkinson.
The severity of Danny Welbeck's ankle injury will feel more unkind as he is out of contract in just seven months' time.
The Gabon global subsequently missed a number of chances as the Gunners failed to break down their Portuguese opponents, though the draw was enough to secure their place in the knockout stages.
"He's a player I rate really very highly".
"The worst news tonight is these injuries", the Spaniard told a media conference.More news: Facebook Messenger to introduce new 'delete sent messages' feature
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Wenger left the club in the summer after 22 years in charge and was replaced by former Sevilla and Paris St-Germain boss Emery.
The Gabon striker was certainly Arsenal's liveliest attacking outlet and he sent another shot just wide of Renan Ribeiro's goal as Arsenal looked to snatch the lead.
Despite drawing a blank, Aubameyang, who joined from Borussia Dortmund for a reported £55 million ($72m) in January , still has nine goals in 14 appearances so far this season - including four from the substitutes bench.
Arsenal struggled to get into top gear against Sporting, but they did have decent chances to snatch a win that would have guaranteed a top spot in the group.
Petr Cech of Arsenal looks on ahead of the Premier League match between Arsenal FC and Liverpool FC at Emirates Stadium on November 3, 2018 in London, United Kingdom.
Joe Cole also shared Keown's opinion in the studio, saying: "He is so talented he has such good physical attributes but he needs senior players pushing him on telling him how good he can be because his goal scoring record is good but he sort of flits in and out of games".