Either a mistake was made when you checked in by an unknowledgeable agent or the written policy is incorrectly worded. I believe you are due a refund of those charges based on the description below and would take this up with SWA. Click on the blue Contact Us button at the bottom of the Discussion Forum screen and include their wording.
https://www.southwest.com/help/baggage/special-baggage-sports-equipment:
Any of the items listed below may be checked in substitution of one piece of the free checked baggage allowance for you at no charge on a one-item-for-one-bag basis. If the item of sporting equipment exceeds 50 pounds in weight, excess weight charges will apply. If the item of sporting equipment exceeds 62 inches in size (outside length plus height plus width), excess size charges will not apply.
Snow ski equipment.
Snow ski equipment, including skis or snowboards, ski boots, and ski poles are allowed, including one pair of skis or one snowboard, one set of poles, and one pair of ski/snowboard boots packed in a container(s) acceptable to Carrier. When substituting ski equipment for a free bag, we allow up to two bags (containing one set of snow skis, ski poles, and ski boots) to count as one item, even if they are packed and tagged separately. Snow ski equipment packed in a plastic bag will be transported only with a limited release of liability.
