Milan, who are battling in ninth in the Serie A, are the only team from the top flight who reached the knockout stages.
Prandelli said Juventus' clash at Galatasaray should have been postponed by more than a day after the weather in Istanbul damaged the pitch.
"I'm bitter about the Champions League," he told Tuttosport.
"All three could have qualified, yet only Milan did it by playing a game of suffering.
"Napoli were unlucky and to go out in that way was sensational. Meanwhile, Juventus were damaged in Istanbul.
"The game should not have gone ahead and it could have been postponed, there was time for that."
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