It has been my experience that it isn't that difficult to ask for fees to be refunded, even when they are legitimate fees.
Here is my example from this morning:
I signed up for a checking account from Citizen's Bank for the $125 sign up bonus. There is a $9.99 fee associated with the account unless you have 5 transactions a month. Therefore, I go in once a month and withdraw $20 5 times and immediately deposit $100 so that I don't incur a fee.
This morning I noticed that I was charged a $9.99 service fee. I went over to ask why and it turns out that the 5 transactions are not based on the beginning and end of the month (ie - 5 transactions in February), rather it's based on your billing cycle and mine starts and ends on the 14th.
I had never been explained this, but it was in the details of the brochure I was given and didn't read carefully enough. I asked if they could make a one time adjustment and they refunded my money without any trouble. I then proceeded to withdraw $20 5 times and deposit $100 right in front of him ;)
The moral of the story is to ask for fees to be refunded, even if they are legitimate. The worst that can happen is that they say no.