Nico Paz had Como ahead at halftime before La Dea struck twice through Mateo Retegui to earn the points.
Cesc said afterwards: "I don't know what to say, I saw a different match from you journalists.
"It depends on what you look at: I think of the injury to Moreno, of Perrone who played very well, I'll keep the game, the competition, the desire to do well.
"We have to play like we did today, even if everything changed. I saw that Atalanta struggled a lot, then with their strong bench it is normal that they can make the difference. Congratulations to Atalanta who won."
Asked about tension with Atalanta coach Gian Piero Gasperini, Cesc continued: "A little, I never talk to the referee, he did and shouted often. I think we need more respect, but who am I to say that. I won't say anything else about the referee: we could have managed things and some plays better. Nothing to say, they won the match with the strongest player they have. But it was a tough match, coming here to us is always difficult.
"Injuries? I have faith in all the guys, we work hard to do well, the team is growing and doing many things well. We prepared the game well, it gives me strength as a coach. Proud of them and for what we have done so far."