Welcome to the Community, MelTilk.

Let fix your issue with miscalculated Net Pay in QuickBooks Desktop (QBDT).

I advise updating your payroll to the most recent release. This downloads the latest recent tax rates and calculations into your account and is frequently used to resolve payroll concerns: Update payroll to the latest release

Here's an article that provides a list of common payroll errors and how to fix it: How to fix common Payroll errors in QuickBooks.

You may find the following articles helpful. It provides an overview in case payroll items/taxes are calculating incorrectly:

• Payroll items on a paycheck are not calculating or are calculating incorrectly
• QuickBooks Desktop calculates wages and/or payroll taxes incorrectly 

Let me know in the comment section if you have other payroll questions or concerns. I’ll get back to answer them for you. Have a good one.