While billing all the phases of a project, extra time entries are getting automatically marked up. How do we prevent this?
This can happen when you bill a project based on % Complete of the project by checking the option Generate invoice amount based on % complete value when applicable on the Invoices > Invoice Filters and Options dialog. This can change the Net Bill amount and Core automatically writes up/down the time entries that you are billing based on the changed Net Bill amount. The same thing can happen if you manually update the % Complete value or Net Bill amount in the Create Batch Invoice screen.
To prevent the automatic write up/down for extra time entries, Core provides the option Skip extra Time Entry for automatic write-up/write-down in Global Settings > Billing screen. Check this option and Core will no longer write up the extra time entries automatically.