The type of taxation method selected can also affect the pension calculations. You might want to run the employee’s settings again and double check this information. For further information, please refer to the set up workplace pension section in this article: https://quickbooks.intuit.com/community/Employees-and-Payroll/Workplace-pensions-in-QuickBooks-Onlin...
If everything was setup correctly, I’d recommend reaching out the support team for further investigation. Here’s how:
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