It just makes a warning sound and displays a message if the boarding group doesn't match, and the agent gets a message and prompt to board them or not board them from that scan. If the agent knows beforehand that the person is an exception (like pre-boards that can't get to the front fast enough) they can click to board the right after the sound is made, but couples and such in separate PNR's usually require discussion after the scan, along with active military sometimes, so that's where it gets clunkier.

Caveat -- this was how it worked with the mobile scanning that DCA (usually) uses -- haven't seen it yet with the built-in podium scanners yet.