This is not correct. The Owners have submitted a freight invoice (debit note) and the charterers have unilaterally deducted an amount which they have later admitted that it was exaggerated and part of it must now be refunded.
Hence, if a note is to be issued, this should be a credit from the charterers and not a debit from the Owners. On our part, we do not insist on the credit note if it is an inconvenience for the charterers; we just want the money back asap.
Please take it up with the charterers and ensure that payment is forthcoming.