If you have checked a car calculation from the P11D Organiser against the HMRC web site and there is a difference, it is usually because one of the data points is incorrect or mis-typed.

The appropriate percentage calculation is based on a list of criteria, and having any one of these wrong will change the outcome. The following with have an effect:

Data PointNotes
PriceThe price of the car is a key data point - this is the price of the car including any factory fitted options.
CO2The g/km figure entered can have a dramatic effect on the calculation, especially if the car has a g/km of 50 or under, as this brings the Range into focus (see below).
RangeWith ULEVs (cars with a CO2 of 50 g/Km or under) you also need to add the range - this is the distance that the car can travel on battery power alone - see here.
Fuel TypeThe fuel type HMRC require is rounded down to just three options - "A", "D" and "F". Most cars will fall into "A", with only 'old' diesels marked as "D", and Euro 6D diesels marked as "F". Cars marked as "D" attract a 4% supplement on their appropriate percentage.
Date of RegistrationThis is a new element - as cars registered on 05/04/2020 or before use a different set of lookup tables to those registered after 06/04/2020. Older cars use the NEDC tables, newer ones WLTP. In general, newer cars attract a lower percentage - there is more information on WLTP and NEDC here.
Allocation DatesThe date range of the allocation can also have a big effect - remember that the dates are inclusive, so every day counts!

If you have double checked all of these and you still think there is a discrepancy, then download the HMRC Company Car Working Sheet and enter the figures manually and then calculate. You will either need working sheet 2 or 2B, linked below.