Sec 43B of IT act disallowance

My assesse paid Outstanding GST amount after filing his return but before income tax due date Ie,31/10/2018 (For AY 2018-19).

For the same i shown as Tax Paid within due date and not disallowed it in Computation. Tax paid date 18/10/2018 but return filed in 9/10/2018. Now my assesse got a tax demand  by disallowing the GST amount. Is it allowed or not ? But in audit report Clauses of 43B they mentioned not paid within due date and they not disallowed in Computation. What should we do ? We made payment and go for appeal ? Kindly reply . Thanking you.