Hi Deeps
I think you are not doing anything wrong.
On checking the system I think the employee you are referring to may be marked as a Director.
Directors NI is calculated different to that of an employee. See attached guidance.
https://www.clearbooks.co.uk/support/guides/payroll-2/directors-national-insurance/
Clear Books uses the Annual Cumulative method and the primary threshold is £7956 this year.
Once the Director's income exceeds this limit the system will calculate NI.
Hope this helps. If you want us to check further, please feel free to raise a ticket and I will check and reply.
Best regards
Latha