We currently have an issue where the company that handle our ad-tracking/referral payout track and want payment for the same orders multiple time. They honestly doesn't seem to understand the issue, customer will, sometimes, return to the conversion page (checkout-success page) multiple times, because people are just weird like that.
The fix is super simple: Their tracking pixel receive our order number, all they need to do is accept that it's unique and just tracking the first occurrence. Part of their problem is of cause that they switch to a new platform and didn't migrate any data.
Because many of the amount are so small, they just accept a ton of errors and as you say: "sweep these issues under the rug" because it's just a few cents so who cares. But it adds up.