User has a billable time entry that gets marked as non-billable when creating an invoice.
This is likely due to a write-down of 100% for the time entry. Write-ups and write-downs can be done manually, but sometimes CORE automatically performs them based on the invoice amount and the method of billing used. For example, if you have $100 worth of billable time and want to invoice a customer $200, CORE generates a write-up of 100%. The time entry values match what’s been invoiced. Similarly, a write-down occurs if your time entry value is less than the invoice amount. Check CORE Help Center for details.