I'm glad to have you here in the Community. Let me share why your new invoices are showing as paid and how we can resolve this.
QuickBooks Online (QBO) has a feature that will automatically apply the available credit of your customer to their next invoice, which can cause brand-new invoices to appear as paid.
If you don't want this to happen, here's how we can turn it off:
Go to the Gear icon, then select Account and Settings.
Click the Advanced tab.
Look for the Automation section, then press Automatically apply credits.
Toggle it to turn off the feature.
Hit Save, then Done.
Furthermore, if you want to remove the payment applied to the invoice, we can follow the steps I've provided below:
Open the Invoice and click the Payment link below the payment status Paid in the upper right corner.
Then, tap on the date link.
On the Receive Payment page, click the Clear Payment button.
Hit Saveand Close.
I've added some screenshots below for your visual reference.