QB Issue Resolution:

If your going to keep the money. It’s income. Create an invoice for the overpayment & apply the overpayment to the invoice. Otherwise, refund the money to your customer.

Resolution for Issue 'Customer overpayment for a couple dollars' available: Yes (Solved).
Source: Intuit Community forum.

Customer overpayment for a couple dollars: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for couple dollars
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