it seems the travel agent is refunding the ticket then issuing a new one, normally, if the travel agent is refunding the ticket, the travel agency policies takes upto 15% of ticket price. But happens if the finance department will issue a check for the customer for refund.

Like the post above, verify whos mistake it is.. then proceed from there. If its the agents mistake, i think he/she might be trying to get way from paying from his/her pocket.