We had a customer pay by credit card and Clover only charged $9.96 on the customers credit card when the order was $13.09. Clover allowed the sale to be completed even though the entire payment was not collected. We are thinking that the customer only had the $9.96 remaining on their credit card.
Note that I'm unclear in what context you are asking this question. Note that this is a developer forum. If you are a merchant and wish to dispute with a charge you should contact customer service.
The situation you describe is known as a "partial authorization". Clover's apps will first ask if you want to accept the partial authorization. If the user replies no, the partial auth is voided (made as if it never happened). If they say yes, then the partial amount is charged, and the user is prompted that the order is partially paid and given the option to add another payment. Exactly how this manifests depends on the specific payment flow (register, sale?).
If it's a third-party app accepting the payment, it's that app's responsibility to handle the partial auth.
