Provider applied Bank payment to the Invoice, while payment amount was less than invoice amount. Invoice was closed by applied partial payment, and Order completed.
The issue was caused by the Internal issue PBA-56311. While working with the Add New Payment wizard, provider pressed "Back" button in the browser, and re-enterer payment parameters (with less total than Invoice sum). Previous payment information was still cached, and as the result the payment was created and Invoice was closed.
The issue is planned to be fixed in one of the future versions of PBA-E. As a temporary workaround provider is advised not to use "Back" button of the browser while working in Provider's Control Panel.