Why are the timesheets of some users not auto-populated with Holidays?
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If some of the users timesheets are not auto-populated with Holidays, though they have the same permissions as others who can auto-populate Holidays, then it is more likely a user configuration issue.
The time off type Holiday is not enabled for the users whose timesheet is not auto-populated with the Holiday.
Enable the timeoff type Holiday under Time Off section of the user's profile.