It could not hurt to contact the organization responsible for granting the fellowships, expressing your concerns, and requesting a refund of your fees.
The collection of fees sounds like it was automated - it's not like the old days where you'd send in a check by snail mail that they'd cash. Humans have a little bit more heart, and occasionally take pity if an application, for whatever reason, is not going to be processed, and waive the fee.
It cannot hurt to write a polite and respectful letter or phone call enquiring about the process and your concerns. There may be some detail that you overlooked, or some glitch in the application process that invalidated your application but still charged the fee(s).
I cannot stress enough that it is very important that you be extremely polite, as you may qualify to reapply for this fellowship at a later date, or the person you contact may have some suggestions about other resources that match someone with your qualifications. It is very important that you be polite and understanding, rather than approach with the assumption that the whole application process is a fraud.