Time entries logged against a sub-phase are not appearing when you generate an invoice, even though time has been entered for the billing period.
This can happen when time entries logged against a sub-phase are not approved. In CORE, only approved time entries are eligible for billing. If a sub-phase does not have the Auto-approve time and expense entries rule enabled, time entries logged against that sub-phase remain pending. As a result, those entries are excluded when generating invoices.