As one who has found her Y seat 'crossed out' and a lovely single digit seat hand written in on more than one occasion, and have had my listed RTC jumped into WBC, it can happen.

The best way is to quietly/nicely let them know you're flying non rev, and request it once at the gate when the agent isn't being swamped by 'elites', then go sit down a discrete distance away, ignoring the screaming thoughts that are saying 'Oh no! They've forgotten about me!' as other pax are loaded on.

Often as not I've found that if I'm the last one on, I'm getting the very best seat... FC, exit row, or even the last seat with a 'free space' next to it on the fuller flights, probably in part because I was one of the few people who treated the gate agents with a scrap of decency in a world of *gimme gimme gimme*!