Hi @NealRM,

I can think of a few possibilities as to why this is so. Let's go through them one at a time.

You mentioned a different invoice was paid. I suggest checking this specific invoice if the payment was recorded correctly.

Here's how:

1. Highlight the Sales tab.
2. Select Invoices.
3. Search for the invoice in question, and click it.
4. If it's paid in full, leave it as is. 
5. If it's not paid at all, then you'll need to correct this by transferring the recorded payment from the other invoice showing an incorrect balance.

Follow the steps below to transfer the recorded payment from one invoice to another.

1. Go to the Sales tab.
2. Tap Invoices.
3. Locate the invoice in question.
4. Under the Paid label, click the link that reads 1 payment made.
5. Click the date that appears as a link, this will open the Receive Payment window.
6. Uncheck the incorrect invoice under the Outstanding Transactions section, then put a check on the correct invoice. 
7. Press Save and close when done.

If you've recently created a credit note transaction for this customer in question, you can follow the same steps I provided above to see if it was automatically applied. In QuickBooks Online, there's a feature that automatically applies customer credits to open invoices. 

If this is the case, you can disable the feature to avoid this from happening again. Here's how:

1. Go to the Gear icon.
2. Select Account and Settings.
3. Tap the Advanced tab.
4. Search for the Automation section. Uncheck Automatically apply credits.
5. Click Save, then Done.

Following the same steps above on how to transfer payment, you can uncheck the payment to remove the credit from the invoice.

If your situation is a little bit different than what I provided, I'd appreciate it if you share more details. It's best if you can add a screenshot as well. 

On the other hand, if you have issues locating payments in the Bank Deposit page, you can refer to this article: Find missing payments you want to deposit in the Bank Deposit window. You'll find 2 separate sets of steps, as well as screenshots for your reference.

Feel free to post a comment below, should you have additional queries. I'll be sure to get back to you.