Awful online booking experience

On booking international flights, I captured my full names and surnames on the Flight Centre booking platform as they appear in my passport. It would apprear that the system parameters are limited to only a first name, middle name and surname. When my e-ticket was issued it indicated my first name and used my third name as my surname. On noticing the error, I contacted a Flight Centre's service agent only to be advised that this could not be changed. I would have to cancel the booking, incur a penalty and apply for a refund. I would then have to rebook and pay for the flights again to correct my details. It is extremely unfair to be punished in this way for system limitations. Not happy!