But it was Welbeck's injury just before the half hour mark that was the main talking point from a largely forgettable Emirates Stadium encounter.
Such was the distressing scene a number of his team-mates had to look away before the popular striker was carried off to applause from the whole of the shocked Emirates.
"He was working well and he was having a good match", said Emery.
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".
Meanwhile, Carl Jenkinson and Emile Smith Rowe get another opportunity to impress.
But Arsenal did secure a last-32 spot regardless, as Vorskla Poltava lost 1-0 at home to Azeri outfit Qarabag in the other Group E game.
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"They have scored goals and created a few too, maybe even more than Kovacic, but that should not hide the effect he has on the team".
The move to replace the manager was precipitated by Danny Welbeck's victor in Arsenal's 1-0 win over Sporting in Portugal two weeks ago at a raucous Estadio Jose Alvalade.
Welbeck had to be stretchered off with oxygen in the Europa League tie, as teammates looked on in horror.
Arsenal midfielders Matteo Guendouzi and Aaron Ramsey were both visibly upset after Welbeck, who is out of contract at the end of the campaign, went down after jumping to win a header. His injury also affected the mentality of the players as they could see it was a big injury.
And while Nelson may not be a ready-made replacement for Welbeck, Emery says he is keeping a keen eye on his progress.
"He's someone who really know what he wants from each player", said Mustafi.
Jeremy Mathieu was sent off late on for the visitors, and he will miss the next game.