Check the number of days between payment and refund. This behavior happens because the payment was voided instead, and then collected at the new lower value.
This happens when a refund takes place within a few days after the related payment was issued. Stax Bill will first attempt to void the payment, then re-issues the payment with the lowered amount.
While credit card transactions are authorized immediately for transfers of specific amounts, it still takes a few days to resolve. Customers will typically see this first as a pending transaction on their credit card statement. Once resolved, the end customer will only see the re-issued amount on their credit card.