NITs and IITs follow decentralised & autonomous selection process for Ph.D scholars. This process of giving more liberty to these institutions had yielded to NEPOTISM (Favouritism or Partiality). Departments inside institutions have good understanding between the professors of the institutions and select students even before the selection process starts virtually. 

The consequences of decentralised and autonomous methods in student's selection are:

1. Any eligible candidate will not be selected.

2. Reseration will not be followed - even for totally deserving students from quotas.

3. central government funds will be misused and national growth in research deliberately put to spoils.

There is speculation whether reservation policy is properly followed. Sc/ST/OBC/Minorities are present in very low numbers in Ph.D @ NITs and IITs. 

To the graetest horror even quailified and deserving candidates of OC are suppressed to give way for the kith and kin of the professors. This is happening as a mafia.

 https://www.youtube.com/watch?v=xb_wq9PYzp4​

https://www.youtube.com/watch?v=JgF5fSyyvpk​

https://www.youtube.com/watch?v=v9U5Ad6zhbg​

http://timesofindia.indiatimes.com/city/trichy/Nepotism-alleged-in-NIT-T-PhD-candidate-selection/articleshow/53583357.cms​

http://www.dtnext.in/News/City/2016/08/05224326/Exstaffers-RTI-shows-fraud-in-NIT-admission.vpf