Why doesn't the IRA I set up calculate right?

Thanks for sharing your concern here in the Community. I can share some insights about your IRA calculation concern in QuickBooks Online (QBO).

You'll want to review the computation for your deferral and employer contribution and ensure to include bonuses, overtime, commissions, and all other compensation categories to calculate the deduction. Also, the amounts you or your employees contribute to a retirement plan must be reported on Form W-2. So the next time you pay your employees, make sure the retirement amounts are showing in their paychecks.
 

Please see this article for more details in managing IRA in QBO: Set up a retirement plan.

I've also added this link that includes a lot articles for future references in managing payroll and taxes in QBO: Employees And Payroll Taxes.

Please feel free to post a reply if you need further help managing retirement plans in QBO. I'll be happy to help you. Take care!