I just filed my taxes and I wanted to pay for my turbo tax service with my refund, I have done it like that the past 6 years and this year my bank was charged.
If you got charged the fees it is too late to change that. But at least you saved the $40 Pay with Refund service charge. Maybe your refund wasn't enough to cover the fees plus the service charge? Did it offer you the choice to pay with refund? You should always assume anywhere you enter your credit card for anything it will charge you right away.