According to the T&Cs you must use your card for a purchase at least once during each billing period in order to keep miles that are more than six months old from expiring. Did you perhaps go more than one month without using your MasterCard? If so then Spirit can wipe out all miles which were earned more than six months prior without warning. It doesn't look like you have any recourse in the matter since it is in the T&Cs of the program and was probably included in the T&Cs for the card when it was first mailed to you. The first time you used the card you agreed to those T&Cs. Sorry but it looks like your miles are gone for good.
If I may add, this program, quite frankly, sucks. If most of your mileage earning activity is from credit card use you'd be much better off with one of the legacies to earn miles for a trip to South America.