Hi Lisa, thanks for posting on the Community
As an employer, you may need to report and pay tax and NI on any benefits you pay to your employees. To view the full list of benefits and their specific NI obligations, click here.
If you're using a benefit that should be deducting employer NI, please get back to us below with the specific benefit that you're using and the version of QuickBooks Online Payroll that you have (Standard or Advanced).
If you ran a draft run of the payroll before adding the benefit, please delete this and re-run to see if it takes the changes into consideration for the NI deductions.