Let me help you fix this, @amyk3448.
It could be that the vacation item that was set up was under the regular pay instead of vacation pay. This is the reason why the vacation hours weren't deducted from the total accrued vacation hours.
To fix this, we can go back to paycheck and replace the vacation pay with the correct payroll item. Here's how:
Once done, you can now enter the vacation hours used by your employee. This will now deduct the total available vacation hours. Then, you can save the changes that you've made to this paycheck.
In addition, you can also run the Paid Time Off List report to check the available and used paid time off hours of your employees. Just go to the Reports menu and select Employees & Payroll. Then, click Paid Time Off List.
If I can be of further assistance, please let me know by posting below. Hoping this response finds you with a smile.