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   The holiday time off bookings are missing on statutory holidays for some users though Holiday Time Off Type and auto-population is enabled.

The Holiday auto-population is associated with the timesheet of a user. Only if a timesheet is available for that period will the Holiday be auto-populated, booked and approved automatically.
The users for whom the Holidays are not booked and approved automatically, would not have timesheet permission enabled. Auto-population would work only if timesheet is enabled for the user.

Enable timesheet permission for the users.