Quickbooks payroll double paid a bonus to my employee. How do i make sure this never happens again?

Hello there, pathcoffees.

Thank you for posting here in the Community. I'd be glad to assist you with about double-paid bonus to your employee in QuickBooks Online. 

I would like to confirm if this is a direct deposit or a manual paycheck. If this is a manual paycheck, you can simply void the check. Here's how:
 

1. Click  Expenses.
2. In the Expense Transactions list, locate the check to void.
3. From the Action column, choose Void from the View/Edit ▼ drop-down menu.
4. When prompted, hit Yes to confirm you want to void the check.

If you can't void or delete the duplicate transaction, I'd suggest contacting our Payroll Support Team. They'll pull up your account in a secure environment and help you with this one. 
 

Here's how:

1. Click the Help icon on the top right. 
2. Tap the Contact Us button at the bottom. 
3. Enter a short description of your concern. 
4. Tick Continue. 
5. Choose Get a callback to connect with our support. 
    

To prevent this from happening in the future, ensure that all the information entered is accurate when creating paychecks.

In addition, I've also added this article that will help you manage an overpayment of taxes: Resolve a payroll tax overpayment.

Feel welcome to get back on this thread if you'll need assistance in dealing with payroll tasks. We're always here to help you.