If you have supplementary paper in 12th board, then yeah! it can affect your admission to the universities or other entrances as most of the cases, the eligibility suggests that the student need to pass all the subjects with some minimum qualifying mark defined by the university.

So before filling application forms, please read the eligibility criteria in details to be sure about that you are eligible for the course.

I hope my answer provides you some hint. Wish you a great eve!