AR: Invoices are with the Negative freight amount. what does this mean.

We are having some invoices shows open with the negative amount. receipts have been fully applied to the invoices, but the invoices have a negative freight amount and this balance stays open. how we should have applied the receipt to the negative freight value?

   here is an example:

        Original invoice is for 419.73. there is a negative amount on the freight line (12.01). So, the total due on the invoice is 407.72.

          customer Paid: (397.40). we had to adjust (14.22) and (8.11) was the discount. this leaves the exact freight amount (12.01) on the invoice.

how this receipt should have been applied if the above method is incorrect?