You've come to the right place, @StoneCo.
When recording customer's payment via the bank deposit window it will not be applied directly to the open invoice. You'll have to enter the customers' payment via the Receive Payment screen and match it with the deposit transaction. By doing so, you'll avoid getting duplicate records and ensure your transactions are matched accurately.
To resolve your concern, let's generate the reports mentioned by @Teri to verify how many times the transactions were counted. Once checked, delete or unmatched the transactions that caused the duplicate records.
To record your bank deposits in QuickBooks, you can refer to this short video clip:
Once completed, let's make sure that payments are recorded and applied to the invoice properly.
Lastly, you can now match the customer's payments with the deposited transactions.
For more insights about managing your transactions, you can refer to these articles:
Always feel free to visit us here in the Community if you have other questions. I'm just a few posts away.