All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger. We ask Allaah to exalt his mention as well as that of his family and all his companions.
If the regulations of the company where these employees work entitle them to transport fees as a part of the wages that is agreed upon with the company, meaning that the company offers them a transport bonus, then they can use any kind of transportation and keep the difference. But if the company authorizes them to buy a ticket, and this is what appears from the question, then they are obliged to give back any excess money, as in this case they are agents and any excess money is to be given to the authorizer not to the agent.
Allaah knows best.