User updated the fee schedule after the time entries were entered. The bill rate did not reflect on the invoices created.
This happens because the rates on the invoices are drawn from the Time Entries screen. Updating the rate at the activity item level does not affect the existing time entries and, therefore, the invoices. The Time Entries screen itself draws the rates according to the rate hierarchy (Rates in CORE). For existing time entries, you need to use the Actions > Update Rates option to update the rates. Check out this article for more on that: Updating rates for time entries.