Basically it all comes down to what did your customer authorize? We have a few restaurants around here that charge service fees for using a debit / credit card. A favorite restaurant of my wife and kids is a stand alone shop. They charge % fee to help cover their cost. It annoys me (why am I paying you so that I can pay you?) but I understand it. There is a very clear sign at the register and it shows on the final bill - so I authorize these charges. While annoying, I can't dispute these charges under Reg E. Is this a similar scenario to your customer? If so, the fee is authorized.
This is a completely different situation if I never see this charge until the bill settles against my account. My bill is presented to me for $100, no mention of a service fee, and I swipe and sign for $100 - but the charge settles for $105, there is a Reg E claim for $5. I authorized $100, had no knowledge of the extra $5, and it was not included on my bill. I can't dispute the $100, but the $5 is covered by Reg E.
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