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:
Click on Help at the top menu bar.
Hit on the Contact Us button.
Enter a brief description of the issue in the What can we help you with? box.
Press on Let's talk.
Select on Geta callback.
Key in your contact details, then tap on Confirm my call.
I've also added here some links about managing PTO's in QBO for reference: