Some scanners (such as all Kodak scanners) have an internal image buffer to make them faster. If you put more than one batch in the scanner, these scanners scan a few extra pages after a batch is complete. These extra pages are saved in the scanner’s image buffer.
If you click New batch in the dialog, the extra pages are handled correctly. You do not have to do anything special.
If you click Stop, you must remove the extra pages that were not in the batch from the scanner’s output tray and keep them with unscanned invoices.