The midfielder was left out of the squad for Wednesday's match at Stadio Artemio Franchi, and veteran trainer Zeman said he believed the rest of his squad would step up in the former Fluminense player's absence.
"Marquinho has not been called up for the Coppa Italia. He did something that he should not have done," he told the Roma Channel.
"But I have confidence in the rest of my players."
The former Lazio coach also praised the work done by Vincenzo Montella at Fiorentina and rubbished claims that the top clubs do not care about cup competitions until they are close to winning them.
Zeman continued: "They are a team that play good football. They have lost their last few matches, but that's only because they failed to exploit their chances.
"In other countries this type of competition is very important. But in Italy it only seems important in the latter stages. For me this competition has always been important."