The SA302 tax calculation is solely a calculation of your tax liability for the year, based on the entries in your tax return. At this stage, payments on account or any other payments are not included.
When your tax return is captured, your Self Assessment statement is updated with the results of the calculation and payments on account are applied at that stage. Hopefully, the payments on account have covered all or most of the liability, so the only a small balancing payment is due. There is guidance on payments on account here:
Understand your Self Assessment tax bill