User is creating a manual invoice from approved time and expense entries, but the entries are not marked as billed and still show up in the WIP.
This can happen if the options Link Approved Time/Expense Entry are unchecked when you create the manual invoice from approved entries. In that case, although Core creates the invoice from the approved entries, it does not link the entries to the invoice and they remain available for future invoicing. To link the entries to the invoice and mark them as billed, you should check these options when creating an invoice. Check the Core Help for details.