I've seen it happen, both for mainline and for RJs where people walk or are bused to a cluster of baby airplanes parked on the tarmac.

If I'm jet lagged, running late, or not awake for a morning flight, I always verify the destination with FAs as I board. I've even heard the lead FA and pilot state the wrong destination during the pre-flight announcements, which sometimes leads to a big gasp and panic. One time someone even announced that we were about to land at the wrong airport.

My guess is that some of the problem is GAs not paying enough attention when then scan boarding passes, perhaps combined with passengers tending to race ahead to the jetway as soon as their boarding passes have been scanned. I say this because I notice GAs shockingly often not noticing the exit row alarm on the scanner and therefore failing to verify that people are exit row qualified. When I'm in an exit row, I volunteer that it's OK more often than not, and the GA usually looks a little surprised. When I notice during boarding that someone else is assigned to an exit row, it seems about 50-50 whether the GA notices or makes the required inquiries. It's worse on small RJs.

If the GA can miss the obvious exit row alert, I would guess that they can equally fail to notice or ignore an indication from the scanner than the passenger is boarding the wrong flight.