When setting up Holidays, remember to check the "The office/business is closed for this event" check box if you DON'T want your employees to be able to clock in on that day. This rule applies to "Auto Clock-In" as well.
If the office is not closed on the holiday, and you would only want certain employees to clock in, you can go to Preferences --> Personnel/Employees and configure specific employees' "Eligible for paid holidays" setting. If employees are eligible for paid holidays, there punches would be accepted on holidays if the Office is open.
See the attached screenshot for examples on both these options.