See technically there must not be any problem, but due to the discrepancy in the information it may cause some minor confusions for that it won't be a big problem. If you have your name correct on the EWS certificate, then you have nothing to worry about. If all the documents have the same fathers name i.e., with the middle name then also you won't feel any problem. Now if you feel insecure then you can visit the DM office with a xerox copy of your EWS certificate and get it attested by the DM stating that the name Prinuj Kumar Aggarwal and Prinuj Aggarwal is the same person.

To know more about JEE MAINS counselling visit the link below:

https://engineering.careers360.com/articles/jee-main-counselling

I hope this answer helps. All the very best for your future endeavors!