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This happens when one recorded a received payment through the invoice and a separate deposit transaction. An added bank transaction is also a separate deposit (cash in) in the bank register.
To resolve this, you'll want to check which of the payments is linked to the invoice and delete the other one, or delete them both and recreate the invoice payment. The other latter is much easier compared to finding w/c of them is linked to the invoice.
Let me know if you need more help with your transactions.