Question

why did sultans and mughal on whole considered kolis rebels and criminals

Answer 1

The Kolis belonged to the marginalized sections across the regime. During the times of Delhi Sultanate and the Mughals, they were termed criminal as very often they joined the irregular armies, those looking for political gains. Owing to this reason, they were always a reason for trouble for the rulers.
Even during the times of the colonial régime, the tribe was considered criminal and was placed under the Criminal Tribes Act of 1871 as a denotified tribe, since the regime felt that people from this tribe indulged in non bailable offences often.