The scanner itself does not do any processing of the information.
It is an image reader that is connected to one of the gate PC's that runs the Gate Reader application. The application communicates with the back end server, that interacts with the Host (SHARES) {attn SHARES haters, the gate reader does not directly interact with SHARES} and opens two boxes. When the application is opened, all the names for the flight are in one box (un boarded). As a boarding pass is scanned, the name moves to the other box. (boarded) At the end, the agent selects "reconcile' and only the names of those who scanned are rectified back through the back end, to the Host.

The agent opens the flight to be boarded. The reader scans the barcode and transmits it to the PC, which interacts with the Gate Reader application and matches the scan to the record of the passenger, and (assuming they match), the Gate Reader flashes green, an audible confirmation is goven, and the name is moved on the agent's screen to the "boarded" box. If there is not a match, a warning response is received. (Different sounding beep than for a match, the Reader displays a red light, AND the application displays a pop up window with the mismatch/error.

I can't think of a scenario where a boarding pass for a flight other than the flight boarding would not result in a audible alert and a visual alert to the agent boarding the flight is displayed.

Other than the application moving someone to the "boarded" box via an automated scan, there a couple ways that the agent can move the name to the "boarded" box. Both involve manual intervention based upon information that the agent obtains from the boarding pass.. This is available in the event that the reader is not physically working, or the barcode is unreadable. One is entering hot key (or clicking on the menu) and entering the Sequence Number. The other is to select/highlight the passenger's name on on the "unboarded" list and select to move it to the boarded list.

Sequence number discussion in above posts. If an agent looks at a boarding pass for only the sequence number (does not verify the flight printed on the pass) , and enters it, it will move the corresponding name to the "boarded list" ONLY if that name has not yet been moved. There would be an audible warning and visual display to the agent if the name associated with the sequence had already been scanned/boarded...or when the correct person's pass is scanned after the wrong person (like from another flight) had been manually entered. In the case of the first item the agent should look at the name on the boarding pass (if they didn't happen to note the flight number was wrong) and observe that the name does not match the sequence for THAT flight.
There are multiple safeguards built into the system, to avoid boarding a person to the wrong flight. When operating in fully automated (scan and process) mode, I can't think of a scenario that allow a the wrong person to avoid. If any of the manual processes are used...the failure would come from the operator, not the application.