I think this season Liverpool are not playing well, or maybe you could even say bad, with their match yesterday which they lost badly to Atalanta, I don't think they will be able to qualify, even though there is a chance to qualify, but it feels almost impossible. Liverpool did attack a lot, it's just that Atalanta were more efficient in the game, even though they didn't attack much, they were able to score goals which made Liverpool lose the match. I think Liverpool are having problems, but I don't know what the reason is, they are experiencing a decline in performance.
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Liverpool are in the championship race in the Premier League and this must have also had some side affects for them in the Europa League. Because Klopp had to rotate the squad a little for the Atalanta match. However I believe they still played really well. I mean they created a lot of goal chances but weren't having their best day though.

3-0 is a score that is really difficult to come back from. More importantly, Liverpool have a PL match only 3 days after the second leg against Atalanta.
If the players' minds get busy with thinking of that match then it would be near impossible to eliminate Atalanta.