I have just discovered 2 employees were paid for leave that they didnt have and there was no warning when I did the payrun. Has anyone any ideas why?

Hi there, @clmuir.

I've got some insights to share about running paychecks in QuickBooks Online.

When creating paychecks in QuickBooks Online, the system will not recognize if there are leave credits used, which are not intended for the employees. 

To get this issue sorted out, I recommend verifying the details on your employees' paycheck. The number of working hours might be entered on the paid leave section, which can be the reason behind this matter.

Once verified that the set up is correct, and the problem continues, I suggest contacting our Customer Care Team. They have the tools so check on your settings and identify the root cause of this issue.

To do that:

1. Click on the Help (?) icon.
2. Select Assistant and enter Contact support in the chat field, and then click the Send icon.
3. You'll be asked about your concern, and you'll need to enter and send it.
4. If you can't see any related topics to your issue on what they shared, select No, get me a human.
5. Then, click Contact Us.
6. Choose either Callback or Chat.

To check the availability of our live experts, please visit this article: QuickBooks Online support hours.

I've also added here some links about managing PTO's in QBO for reference:

• Cashing out annual leave
• Annual leave payroll tips with Quickbooks Online and Keypay

I'll to assist you if there's anything else that you need. Just let me know by leaving a reply below. Keep safe, clmuir.