There are times that your browser is full of frequently-accessed page resources, thus causing websites, like QuickBooks Online (QBO) to act weirdly. This can be the reason why your invoice mark as paid.
Let's consider accessing the website and logging into your account using a private browser so we can isolate this issue. To do so:
Google Chrome: Ctrl + Shift + N
Mozilla Firefox: Ctrl + Shift + P
Safari: Command + Option + P
If this works, you can clear your regular browser's cache so the system can start fresh. But if you get the same results while using a private browser, use a different browser app to roll out the possibility of a browser-related issue.
If the same things happen, please check that you do not have the automation feature enabled which will automatically apply any credits on the customer account as payments, by going to the Cog Wheel > Account and settings > Advanced > Automation > Automatically apply credits.
I'm more than glad to offer future assistance to you in the future. Simply go back to this thread and add some details regarding the issue in QuickBooks Online. Have a great day ahead and stay safe!
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