> In the event that Apple receives any notice or claim from a payment provider [...] Apple will have the right to retain its commission on the sale of that Licensed Application, notwithstanding the refund of the price to the End-User.
"From a payment provider" means a chargeback, e.g. a customer calls their credit card company the charge was fraudulent, and the credit card company files a dispute code against payment provider (usually Visa 83/JCB 546/Mastercard 4853/Mastercard 4863 depending on the case). In this case it's not uncommon to not refund the fee. In fact, many payment providers will also charge you extra fee for the dispute (e.g. Stripe charges $15[1]).
There's also filing fee in case the merchant trying to fight the dispute and lose. The fee varies by network: $500 for Visa, at least $600 for Mastercard.