User has many expenses on the projects that are getting automatically flagged as Extra.
By default, Core marks the expense entries of all projects as Extra and always charges them on top of the contract amount (in addition to the contract amount). To avoid this, you need to apply the rule Include billable expenses in the contract amount to your project. Also, if the combined value of your billable time and expenses becomes equal to the contract amount, Core marks any new expense entries as extra and any new time entry as non-billable even if this project rule is active. If this continues to be an issue, you can batch update the Set Extra flag to False in the Expense Entries screen for all the extra expenses before billing them. Check the Core Help for details.