The software will not take a deduction
Payroll will not take a tax-deferred deduction if there is no taxable pay.
To work around the issue, pay the employee $1 in taxable gross pay.
To avoid paying the employee an extra dollar for each payroll, create a deduction to withhold $1 using the same general ledger account that was used to charge the gross pay.
You must edit the employee's W-2 at the end of the year to avoid overstating gross wages.