The Giallorossi took the lead in Bergamo through Edin Dzeko, but second half strikes from Jose Luis Palomino and Mario Pasalic turned the game around for the hosts.
“This is not an easy ground to play at," Fonseca said.
"Atalanta are an excellent team who always create lots of openings. We didn't concede many chances today and defensively we did well. The problem came after we let in the first goal – it suddenly became difficult for us.
"The same thing happened after the second goal. I have no complaints about the team's attitude today. The game was decided by small details but defensively we performed well.”
Is this defeat a setback for your hopes of qualifying for next year's Champions League?
“We have another 14 games to play and I believe we can still do it. It's difficult but all the teams are dropping points this season. The league is very evenly balanced and I think it's possible.”
What happened on the two goals? Do you think Atalanta were stronger physically in the second half?
“It's a mental issue. Physically we're in good shape. In the last two games we've played at a higher tempo than on other occasions. It's not a fitness problem. We must believe we can get back to producing the great performances we were before.
"It's hard to explain why you concede certain goals but at the moment it seems that every shot is going in. We've let in three from corners in our last few matches but looking at our performance today I'm confident we'll soon get back to winning ways. We must work hard, as we did this week, so that we can win our next game and turn things around.”
Do you think there are some positives to take today from a tactical perspective? You seemed to be more reactive and afforded Atalanta few chances.
“This was a different game to the others. I can't say we'll always play this way against other teams. The intensity on the ball is different because Atalanta are so difficult to play against but we could use the same system again. We were missing [Bryan] Cristante today as well as [Amadou] Diawara, so [Gianluca] Mancini was our only option for the holding role.”
You were very careful to limit the space available to Atalanta and held a very high line. Was that something you asked the team to do?
“It was important for us not to get stretched. We needed to stay compact when defending and we nearly always succeeded in doing that today. Unfortunately, once we regained possession we weren't able to do the things we'd practised and get balls in behind their backline. It's not easy against Atalanta though.”
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