GSTR-9 is the compilation of data filled in GSTR-3B and GSTR-1. The information required to be filled in the GSTR-9 form is:-
1) Outward supplies and tax payable in the annual return.
This information could be extracted from GSTR 1 form.
2) Inward supplies, input tax credit and the net tax paid in cash.
This information could be gathered from Form GSTR 3B.
The values mentioned in GSTR-3B and GSTR-1 must align. If there is any difference, then they are required to be adjusted to subsequent returns filed up to September-18 as per circular 26/26/2017-GST dated 29th December 2017.
It looks like while drafting the form, it has been pre-assumed that Form GSTR 3B and Form GSTR 1 would be in consonance with each other, but this may not always be true.
In a condition where the values available in Form GSTR 3B and GSTR 1 does not match with each other, one may arrive at a differential value of tax payable and tax paid as per annual return. A clarification from the Government could be asked regarding the manner of payment of any additional liability (if any).
However, if anyone faces such a situation, then the additional tax liability may be paid through Form GSTR 3B of the subsequent month/Form DRC-03.