Arijit, only Candidates of Jammu and Kashmir and Leh can submit their NEET applications offline as in pen and paper mode. Candidates from the rest of India need to fill in the applications online. So it is not clear if you are from Jammu and Kashmir and filled up the form in Blue. If that is the case, your application will not be rejected even if a blue ink pen was used instead of a black ink pen. What matters is you complete the application form following NTA's guidelines regarding other criteria.