Sounds like the WX created no shows. It is not unknown for elites to decline waitlisting, so the inflight crew would have not been alerted (plus inflight crew are not allowed to upgrade passenger). This is an issue you should have raised with the GA prior to boarding and it would have likely been addressed.

If you looked at the waitlist after takeoff, they are cleared on the door closing -- so that is not unusually.

Write in, you will probably get something. but this looks like a one-off issue and not likely to occur to you again.