It could be that your settings for automatically applying bill payments and credits are turned on. This functionality could turn your open bills into paid ones. You can check this by following the steps below:
Click the Gear icon at the top.
Choose Accounts and Settings.
Go to Automation part the check if Automatically apply credits and Automatically apply bill payments is turned on.
You’ll have an option to turn it off if you want. Also, the bills paid with vendor credits are tagged under the payment transaction (I’ve attached a screenshot to visualize this information). To check:
Go to Expenses from the left panel.
Click the Vendors tab at the top.
Select and open a vendor.
Open the paid bill from the vendor’s transaction lists.
Click the payment maid link under PAID then click the Date link.
This will show the screen with the bills associated with the payment. Let me know if you have other concerns about QuickBooks online. I'll be here anytime to help.