To apply a tax code to an order, NetSuite will look up the corresponding tax code based on the nexus in the order from either your taxable schedule or your non-taxable schedule. If one of these schedules is missing, NetSuite will use the other schedule if available.
For example, if NetSuite is trying to look up the tax schedule for a non-taxable order, but the non-taxable schedule has not been created for the nexus in question, the taxable schedule will be used if available. To correct this, make sure all your nexuses have taxable and non-taxable schedules assigned in NetSuite. You can edit your tax schedules in NetSuite under Setup > Accounting > Tax Schedules.