Reading this thread has suddenly reminded me of my own fail-to-board experience - but my conscious is clear.
Colleague (the MD of my client) and I were on Air Canada YYC-SFO, then onto QF SFO to Australia, separate tickets, both HLO, a number of years ago. The AC flight was late and when we de-boarded, we knew that we might be in trouble with the Qantas flight, and made all possible haste to the Qantas check-in desk.
As it happens, we got to Qantas check-in a few minutes before check-in was due to close; the sign still said 'open'. We could immediately see the check-in agent was surprised, and then worried. He tapped away furiously at his terminal. Colleague and I looked at each other and already had an idea as to what was about to happen. Eventually told that we were unable to travel. We asked why (colleague was WP1, me WP), and no good reason given, but immediately offered a US$500 voucher (redeemable for cash), plus overnight at the Hilton and US$150-odd for meals. We gave them a bit of a hard time, for appearances, then accepted.
Of course what had happened is that they decided too early that we were no-shows and had wrongly given our seats away, and they knew it.
As I say, no harm done to us and the plane wasn't delayed - my only regret is that we weren't a bit more mercenary with the compo; we had 'em on toast.