Anything you charge your customer with a margin over your cost should generally form part of your revenue. However in freight forwarding, there may be items that you reimburse from the customer (E.g. duty payment on behalf of the customer). It is recommended you have a separate request for reimbursement of those costs (This is NOT an invoice but a request for reimbursement). If you really need to show them in the invoice, at least, you can include those reimbursement items clearly mentioning they are reimbursements. If not you will have complications with IRD as to VAT and other sales based levy calculations). Reimbursements are not sales or revenue so VAT, etc are not calculated for reimbursement items.
