I appreciate you taking your time posting here in the Community. There are multiple reasons why taxes have different amounts upon paying and filing them in QuickBooks. I'd be glad to share it with you.
Here are some possible reasons:
There is an overpayment.
Adding or deleting paycheck.
If that's the case, you'll need to run the Payroll Tax and Wage Summary report to verify if there's a deleted and an added paycheck from there.
From the left menu, select Reports.
Search the Payroll Tax and Wage Summary report.
In the Date Range section, select the date in the drop-down.
Select the tax to drill down the payroll transaction.
Then, check the taxes from there.
You might want to read these articles to know more about e-file and e-pay in QuickBooks: