QB Issue Resolution:

If they are duplicates, delete them as long as they are in the current fiscal period.  If not, make an adjusting entry and remove them.   To find them, they will be in the customer details and if you open the payment, you will not see a link to a deposit there.

Resolution for Issue 'I have duplicate payments in Undeposited Funds account. Customer has paid, invoice $120, payment $-120, they have a 0 balance in their account. but if I go to chart of account>Undeposited Funds account>not reconciled> I have about 5 transactions there. I don’t understand how this happened and whether or not I should just delete them. If I select Deposit to PNC (bank account) then it will show that I owe them $120' available: Yes (Solved).
Source: Intuit Community forum.

I have duplicate payments in Undeposited Funds account. Customer has paid, invoice $120, payment $-120, they have a 0 balance in their account. but if I go to chart of account>Undeposited Funds account>not reconciled> I have about 5 transactions there. I don’t understand how this happened and whether or not I should just delete them. If I select Deposit to PNC (bank account) then it will show that I owe them $120: 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 duplicate payments in Undeposited Funds account
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Error Recovery for duplicate payments in Undeposited Funds account [Canada]
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