The Giallorossi crashed out of the Coppa Italia Round of 16, 2-2 after 90 minutes, 4-2 at the end of extra time.
But they would've lost by default anyway, as Fonseca made six substitutions rather than the five that were allowed.
“If there is a problem, we have time to discuss that internally. There is a problem," the coach told RAI Sport. “We had a difficult start to the game with the penalty, which was a difficult situation to understand. After that, we created many chances, missed many goals, and then with two players down, it was difficult.
“This is a tough moment, we wanted to go further in the Coppa Italia, but I cannot complain about the attitude of these lads. We have to prepare the next match."
He added: "Over 90 minutes, with 11 men against 11, Spezia didn't create much at all. It's important to have a player with Bryan's quality to start moves from the back and he did very well this evening.
"We lost to Atalanta, Napoli and Lazio because after conceding a goal, we didn't have the mental strength to turn it around. However, tonight I saw the right reaction to going 2-0 down, we got it back to 2-2 and had chances to win it before extra time.
"I think what we created over the 90 minutes should've been sufficient to win the game."