Zeman described the defeat as a "heavy blow" to his players.
"We did very well in the first half, but after the break we settled and allowed our opponents to control the game," Football Italia has quoted Zeman as saying.
"We made three mistakes on their goals and helped Bologna to get back into it. It is a heavy blow for the squad, as we must always be concentrated to get the best result.
"The mistakes came because we were passive in the second half. It's easy to blame the break for international duty, but that's not true. The players do not suddenly forget movements when they are somewhere else for 10 days."
Roma face a trip to Cagliari next Sunday.