The Lupi allowed a two-goal lead to slip as the Bianconeri staged a comeback to win 3-2 at the Stadio Olimpico, Antonio Di Natale scoring the winner from the penalty spot in the 88th minute.
However, Zeman believes that the referee should not have given the penalty as Leandro Castan did not commit the foul he was adjudged to have.
"After seeing the replays, I think it was not a foul for the penalty," he told Sky Sport Italia.
"It has been a bad weekend for referees. People say they don't decide tournaments, but I think on the whole they really can.
"Tonight Pablo Armero spat at [Panagiotis] Tachtsidis with the fourth official a few yards away, yet did nothing. For me, these things are decisive."
Roma are currently sixth in the Serie A table with 14 points from nine matches.