Payment taken and refunded

Our company pays a supplier by monthly direct debit, a payment was taken and was taken again the next day, the company realised their mistake and immediately refunded the second payment. How do I treat this payment and refund?

Pretty much any way you like as the net effect will be zero. You could do it as a prepayment to the supplier and then go to the payment record and “refund balance”, you could treat it as a transfer to and then back from a dummy bank account (e.g. drawings), or use “something not on the list” to tag both transactions to a suitable nominal.