Issue you issued two payments for an employee on one pay run.  The second payment was a manual cheque, to correct the first cheque which for some reason (incorrect banking information, lost cheque), was not paid to the employee.
Solution
 To fix this employee's YTD values, go into Financial Management > Cash Management > Bank Accounts. Click on the List button to open the Bank Account List and select the bank account from which this employee was paid, and click OK.

Then click on the Bank Acc. button and click on Cheque Ledger Entries from the list. This will open the Cheque Ledger Entries for this bank account. Filter on this employee number to view all the cheque ledger entries. You will see some zero dollar entries; these are the created when the Remittance stubs are printed.

You will see the two entries for the employee for Jan 25. You need to void the Direct Deposit entry, as the manual cheque is correct.

To do this, select the entry you wish to void, then click the Check button and click Void Check. From the options, choose Reverse Entry.

This will reverse the payroll ledger entries for this employee, and the YTD values will be correct.