User has some expenses that are being charged as part of the contract amount even though the project rule Include billable expenses in the contract amount is not checked.
This can happen if the Extra flag of the expense entries is not checked. Core includes all those expense entries in the contract amount whose Extra flag is not checked. By default, when the project rule Include billable expenses in the contract amount is not enabled, the expenses are marked Extra and charged on top of the contract amount. However, when you enable the rule, all subsequent expenses you create are not marked extra and are included in the contract. If you disable the rule afterward, the change does not apply retrospectively and any non-extra expenses you created remain as such. This is how you can have non-extra expenses even though the project rule is no longer enabled. To fix this, you need to check the Extra flag for the expenses. Check out this article to know more about that: Charging expenses on top of contract amount.