There are two reasons why your software omits car and company fuel benefits from Form P11D(b):  

The employer isn't subject to class 1A NICs

1. Click Employer, then click Open Employer record.
2. Click Settings.
3. Check whether the NIC Liable checkbox is clear.
4. Check whether any NIC liable from dates apply to the tax year you're processing.

The employee isn't subject to Class 1A NICs

1. Click Employee, then click Open Employee record.
2. Click the Tax / NIC Details tab.

In the NIC Details section, ensure you've selected the Liable checkbox where relevant.

Also, check any dates in the From and To boxes are within the tax year you're processing.

When this information is correct, your software includes any Class 1A NICs for car and fuel benefits on Form P11D(b) if required.