See the discrepancy in name is supposed to be a great problem legally. Because a small change in name legally creates two different persons in documentation. So I would say you should try to fill your form fill up either in your correct name and change your name on the marksheet or you use the incorrect name and make a affidavit of name change to produce if required during the CA.

In general there will be no problem, but taking chance may be risky so try to fix it. Don't left any problems which can be a fatal threat in future.

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