After the recovery of the body, police launched a probe and checked the CCTV footage, in which they spotted Choudhary and the boy.
The girl was sexually assaulted by four men on Thursday night in a room in the Timki area and later by two men in their autorickshaw near Mayo Hospital square, an official said.
The police contested the claim saying the man was riding the motorcycle under the influence of liquor and met with an accident.
An employee of an app-based food delivery firm was arrested by Nagpur city police on Saturday for allegedly molesting a woman.
The relatives of the deceased have alleged the hospital's negligence and also alleged that after her death the hospital was not handing over the body and demanding payment of around Rs 1.5 lakh.
The autorickshaw driver, identified as Laxmikant Savarkar and the child's kin took him to the hospital.
The incident happened on Thursday night when three people on a motorcycle were stopped by a group of four who demanded money from them for liquor, an official said.