What will be Journal Entry

Dear sir,

A credit note is issued by the supplier when there there is difference in value of supply which is decreasing the value.

I presume you are the service recipient. Reverse the expense booked in your books. Debit the Transporter and credit the frieght charges etc.. Make sure credit note is issued in terms of Rule 54 of the CGST, Rules.

A small change its Rule 53 of CGST Rules