The Core Payroll system is producing duplicate checks for each employee each time the payroll is run. How can I stop that?

Let's make sure that there are no duplicate paychecks in QBO, ttwinnovations.

There are times that too much cache or data in your browser can cause errors or unexpected issues when working in QuickBooks Online. 

Start by using an incognito/private browsing session or a different browser. Here are some of the keyboard shortcuts to quickly open an incognito session: 

• Ctrl + Shift + N  for Google Chrome
• Ctrl + Shift + P for Firefox
• Control + Option +P if you're using Safari
• Ctrl + Shift + P for Microsoft Edge

 
Once done, check if the duplicate paycheck is no longer showing up. If you can't see them anymore, follow the steps in this article to delete your browsing history: Clear Cache And Cookies To Fix Issues When Using QuickBooks Online.

You might also need to delete the duplicate paychecks to correct your payroll records. Here's an article as a guide: Delete or Void Employee Paychecks.

Just in case you're still getting the same issue, you can reach out to our Payroll Support Team. They can take a closer look at this to determine what's causing the issue. Check out this article to get their contact details: Contact Payroll Support. 

Feel free to take a look at this article for additional guidance and reference: Run Payroll Reports.

The Community is always here to help if you need anything else. Just reply below or post new questions and we'll be glad to answer them for you.

Hi ttwinnovations,

Hope you’re doing great. I wanted to see how everything is going about removing the duplicate paychecks. Was it resolved? Do you need any additional help or clarification? If you do, just let me know. I’d be happy to help you at anytime.

Looking forward to your reply. Have a pleasant day ahead!

Sometimes it's a bit complicated to use Quickbooks, I took a course on LinkedIn to learn how to manage it, however, I still haven't mastered it.
You can try with:
Clearing the cache.
Delete and re-add everything to the system.