QB Issue Resolution:

When the deposit is downloaded from the bank, you should MATCH it to the payment.  If you ADD, then you get the duplicate.  Here’s a QB Power Hour where I covered downloaded transactions in QuickBooks Online (fast forward to that part if you want to) and show how to ADD, MATCH, set up bank rules and more.

To fix it, you can UNDO the deposit.  Then, match it to the payment.

Resolution for Issue 'We’ve have an issue when our customers pay by check. QB is recording the payment and then it is also recording the deposit from our Bank of America checking account.' available: Yes (Solved).
Source: Intuit Community forum.

We’ve have an issue when our customers pay by check. QB is recording the payment and then it is also recording the deposit from our Bank of America checking account.: 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 America checking account
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Error Recovery for America checking account [Canada]
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