The travel agency is solely responsible for any third party credit card transaction done via their portal, over the phone or email. Frontier has implemented a policy requiring customers of size to purchase an additional seat at the airport if they are unable to sit in an aircraft seat with both armrests down or if they compromise the space of any adjoining seats. Any passenger may purchase an additional seat for their comfort through reservations.
So the bottom line really is just to make yourself as aware as possible of current pricing before you see an agent. You can still get great deals through a good agent (booking online is not always cheaper) and there is no need to be ripped off if you are savvy about your planning. Advice from a good agent on your destination can be invaluable, just take product advice with a grain of salt.