Hello there, @TLC1231.
Thanks for taking the time to post your transactions concerns in the Community.
When it comes to managing the invoices, QuickBooks Self-Employed (QBSE) works somewhat differently. The invoice feature is only used for sending, and collecting payments from your customers. Hence, it'll not be counted as part of your sales or income.
The program will only include the transactions that are categorised as business transactions.
If you're using QBSE, I'd suggest you review your Zettle account and check for any duplicates. Then, follow the steps to exclude or delete transactions.
You can also check out this article to learn more about handling duplicate transactions in QuickBooks Self-Employed.
If you're using QuickBooks Online (QBO), you'll want to put payments into the Undeposited Funds account, then combine them into a deposit. This way, QuickBooks always matches your bank records.
Check out this article to learn more about this process: Deposit payments into the Undeposited Funds account in QuickBooks Online.
Get back to me if you have additional concerns. I'm always around to help you again. Take care!
