My father's name in 12th marksheet and JEE form is Kumar Gond, while in my category certificate it is Gond. Will it create any problem?

Yes, the difference in the name will cause problem in document verification, but it can be solved with a simple affidavit. It should mention both the names of your father and should declare:

That both these names pertain to the same person

That it is true to your knowledge, and

That you're accountable