What you see is the result of using cash basis accounting rather than accrual basis accounting. The income for the sales invoice did not appear until you received 743.68 under cash basis accounting. But the 750.00 sales invoice is still in the system and must be properly handled. So when you enter the credit note for 6.32, Manager has to add the missing 6.32 to the income account before it can be subtracted by the credit note.
To try to illustrate this, I’ve duplicated your numbers in a test business with no other invoices or credit notes. Here is the drill-down on the income account from the Summary with the business set up for cash basis accounting:
Notice that the sales invoice number and description are not listed for the 743.68 credit. That is because the income came from the receipt for 743.68, which did not have a reference number or description, not the sales invoice, as it would have under accrual accounting. Both the 6.32 credit to the invoice and the debit from the credit note refer to the credit note number.
Now here is the identical drill-down after switching to accrual basis accounting:
You see the sales invoice number and description, because that is where the income is from. And the adjustment to the sales invoice from the credit note is not present, because it isn’t needed.
End result: there is no bug and the reference numbers correctly refer to the sources of both debits and credits.