QB Issue Resolution:

In order to zero out the liabilities category of your employee, you’ll need to process bank deposit to reflect the refund amount you received in QuickBooks Online.

 

Here’s how:

  1. Select Plus Icon (+) at the top, and click Bank Deposit.
  2. In the Add other funds to this  deposit section, fill in the following fields:
    Received from: Select or enter the vendor name.
    • Account: Select the Accounts Payable account. (Use the account you used for 941 payment)
    • Amount: Enter the check amount.
  3. Select Save and Close.

For additional reference you can check this article: How to Record Bank Deposits in QuickBooks Online.

 

By doing this, I’d suggest consulting an accountant if you’re not familiar with the process and to ensure your books are accurate.

Resolution for Issue '941 Overpayment Correction' available: Yes (Solved).
Source: Intuit Community forum.

941 Overpayment Correction: 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 941 Overpayment
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Error Recovery for 941 Overpayment [Canada]
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