If the amount of the late payment surcharge is the same according to your records and those of the NTCA, you must pay it!
At the end of the surcharge calculation list, in the field "SURCHARGE TO BE PAID", you can see the surcharge amount to be paid to the NTCA "Late payment surcharge revenue account" no. 10032000-01076985 (tax type 138). In order to fully settle the tax account, the entire amount in arrears on this tax account under tax type 138 (late payment surcharge) must also be paid.