The women said Boko Haram fighters started pelting them when they refused to run away as the army came nearer.
A group of nearly 300 women and children was brought out of the vast Sambisa forest to a government camp.
The military says it has rescued more than 700 people in the past week in an offensive against the Islamist group.
The women said several were killed in the stoning, but they did not know how many.
The survivors said that when they were initially captured, the militants had killed men and older boys in front of their families before taking women and children into the forest.
Some were forced into marriage.
They said the Islamists never let them out of their sight - not even when they went to the toilet.
"They didn't allow us to move an inch," one of the freed women, Asabe Umaru, told Reuters news agency. "We were kept in one place. We were under bondage."
One woman described how they were fed just one meal a day.
"We were fed only ground dry maize in the afternoons. It was not good for human consumption," Cecilia Abel told Reuters. This led to malnutrition, disease and death.
"Every day, we witnessed the death of one of us and waited for our turn," Umaru, a 24-year-old mother of two, told Reuters.
The women and children travelled for three days on pick-up trucks from the vast Sambisa forest where they were rescued, to the camp in the city of Yola.
Through interviews, officials have determined that almost all those rescued are from Gumsuri, a village near the town of Chibok, the Associated Press news agency reports.
It does not appear that any of those released are from the group of nearly 300 Chibok schoolgirls kidnapped by Boko Haram a year ago in a mass abduction that led to worldwide protests calling for the girls' release.
Thousands have been killed in northern Nigeria since Boko Haram began its insurgency in 2009 to create an Islamic state.
In February, Nigeria's military, backed by troops from neighbouring countries, launched a major offensive against the Islamist fighters, recapturing Boko Haram territory taken in the previous year.
Former hostages held by Boko Haram militants in northern Nigeria say some fellow captives were stoned to death as the army approached to rescue them.