The Experiment will be screened in May
But they have denied press reports that the complaints forced the show's launch to be postponed.
One participant described an early version of the show as "the poor man's Big Brother", according to The Guardian newspaper.
Producers told BBC News Online that some contributors did protest that the show did not accurately reflect what went on in the "cells" and that some volunteers got more exposure than others.
"There is no-one that is excluded, but obviously you tell the stories of particular people as they develop over time," executive producer Alex Holmes said.
"Unfortunately, that may result in some people complaining that they don't get themselves enough screen time, but I'm afraid that's the way these things work out."
He added: "It's absolutely not the poor man's Big Brother. In fact, it bears almost no resemblance to Big Brother at all."
The show has attracted attention because of the experiment it was based on, which was later branded "unethical" by the man who devised it.
Filming was cut short by a day to make sure no harm came to contributors.
But there was no violence, Mr Holmes said, although tensions did run "extremely high", meaning the show will be shown after 2100.
"You could only put these things on after the watershed," he said. "They are difficult. There is a lot of aggression, there is a lot of tension, this is a tough environment."
Scientists who monitored the documentary, in which 15 volunteers stayed in the "prison" built at Elstree studios in Hertfordshire, said they yielded "a tremendous amount of scientific data".
Rebellion
Mr Holmes said, for scientific reasons, the show would focus on the volunteers who tried to bring about change.
"We were interested in studying not only control but also rebellion. That was the axis of our study," he said.
It showed that people in the 21st Century felt more comfortable when they were rebelling than when they were in control, he said.
"It reveals what causes resistance in a society as well as what causes authoritarianism. It shows how people can often struggle with leadership and how leadership is a very difficult thing to handle."
The show, to be screened in four one-hour episodes, will be broadcast on BBC Two in mid May.