User has some non-billable time entries on a project that were never billed on invoices. These entries keep showing up on the Work-in-Progress (WIP) reports (Work in Progress and Work in Progress Details) even after the project is closed.
By default, the WIP reports show all the unbilled time entries of the projects irrespective of their billable status. If you want to clear the WIP due to the non-billable entries, you should manually mark those entries as billed using the Actions > Batch Update option in the Time Entries screen or the Actions > Mark Billed option in the Time & Expense Reviewer screen. Check out this article to know more: Marking time and expense entries as billed.
Another option is to use the Billable filter for the reports and set it to Yes in the Reports > Customize Report dialog. Check the Core Help for more on applying filters to reports.