I mistakenly filled in the best of five marks and percentage while filling out the CAT form.

application will be rejected after the interview process....contact support line for this issue

it will def create problem as it was clearly mentioned to fill all 6 subjects and not just top 5

But marksheet has 500 as maximum marks

I guess they'll again open the portal after some time where you need to verify every detail you entered, at that time you can make changes I guess, only few details can be updated I guess.