question

What API are you using to add the discount? Can you provide the request you are making minus any sensitive information (access tokens). Can you provide an order id?

https://api.clover.com/v3/merchants/6ZA5DNC74X5S1/orders/XTQK4G3W583M8/discounts
Body json - { "discount":{ "id":"X2FF8YFS0G48C"},"amount":-1000,"name":"testing"}

Order ID - XTQK4G3W583M8

Order Receipt - https://prnt.sc/249ztz1

When paying for an order which has a discount coupon applied using this API
https://scl.clover.com/v1/orders/XTQK4G3W583M8/pay

{ "amount":499,"ecomind":"ecom","source":"clv_1TSTS4YVkU6TCArfCPWaaZt7" }

If the amount parameter is set for the remaining amount then the payment status shows as "Partially Paid"

But if the amount parameter is removed from body JSON then the user gets charged for the full amount of $14.99.
{ "ecomind":"ecom","source":"clv_1TSTS4YVkU6TCArfCPWaaZt7" }

The ecomm API will properly calculate the total ONLY if the order doesn't already have a total set. So, this is likely happening because you are setting the order's total to a value that doesn't account for the discount (setting the total, adding the discount, not updating the total to account for the discount). Please see https://community.clover.com/questions/29313/rest-api-applied-discounts-on-a-order-doesnt-affec.html for a similar issue. I would recommend that you use the atomic order endpoint to create the order which allows you to create an order in a single request (including discounts) and properly calculates and sets the total for you. Alternatively, you will need to either properly calculate the total after all adjustments have been made (total must account for discount, etc. see https://docs.clover.com/docs/calculating-order-totals) or not set a total so that the ecomm API can calculate and set it for you. With either of these solutions you should not be passing an amount in the order/pay request to pay for the order in full.