Marotta launched a withering attack on referees after his side were denied a penalty in the closing stages of their 0-0 draw at home to Siena on Sunday.
However, Allegri has claimed that he was left utterly bemused by the Bianconeri official's attack on match officials.
"People always say they want to help the referees but then after the first mistake that goes against them, they attack [the referees]," the Rossoneri boss mused ahead of the first leg of the semi-final tie with Juve.
"In one season there will always be decisions for and against, but at the end they even themselves out.
"To reduce to a game to a penalty incident is wrong; we should all be more calm.
"Marotta's words? I do not know what they are borne out of; myself and Milan have a different style."
Addressing Zlatan Ibrahimovic's dismissal against Napoli on Sunday for slapping Salvatore Aronica in the face, Allegri conceded that the Sweden international had been clearly in the wrong but stated that the incident has been blown out of proportion.
"What happened on Sunday was certainly not a nice gesture," the former Cagliari coach admitted. "But you see things like this every Sunday. He paid a little for everyone."
Meanwhile, Allegri revealed that while January signing Maxi Lopez will feature at some point against Juve, the former Catania forward will not start.
The 44-year-old coach also said that injured duo Alexandre Pato and Kevin-Prince Boateng are now just over a week away from returning to first-team duty but added that it is not yet certain when Alberto Aquilani will be ready to make his comeback.
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