1) If Nathan submits the invoice for $40 higher as the HR managers suggested, his actions would not be ethical. He found an error on the invoice and knew he was not responsible for the charges and decided to contact the car rental company to have the charges refunded. Even though the HR manager felt the amount was not material enough to reach their threshold, it is still unethical to overbill the firm when these charges are not justified regardless of the materiality. Nathan should not submit the bill for $40 higher than the contracted amount. He should submit the bill along with a copy of the credit showing the $40 was refunded. The time and trouble Nathan spent getting the amount refunded does not entitle him to an additional $40, therefore it will be unethical to try and recoup the $40 from the firm.
2) The other courses of action that may be available to Nathan would be:
1) When he received the bill and noticed the additional $40 charge, not to mention anything and just submit it for reimbursement.
2) When the HR manager initially told him not to worry about the overbilling and just submit it, he could have done just that.
3) He could have contested the bill like he did and submit the expense report showing proof that the credit was given without calling HR in advance about the initial overbilling.
I believe the best course of action would be the final suggestion of contacting the car rental company as soon as the overbilling was noticed to get the $40 refund. After the refund was confirmed I would have prepared an expense report showing the final amount paid for the car rental and submitted it to the HR