Originally Posted by flatlander

The flight manifest should show you as boarded because the manifest of passengers (used, for example, to know who is on board an aircraft that has an accident) should list you.

It is possible for gate staff to make a mistake and mark a passenger as offloaded at the gate while still allowing them onto the aircraft, but it's a significant error and I have only seen it happen once (to another passenger - the crew did a headcount which didn't come up and we had to have a school-style rollcall of names to find out who was onboard that shouldn't be, since they had a valid boarding pass). That's extremely unlikely, easily less than 1/2000 chance on a flight. Airlines take correct manifests seriously.

I suppose the scanner may not have read your boarding pass and the gate staff didn't notice and let you on anyway. Also, quite a serious error, but I'm sure it could happen on rare occasions.

Otherwise I don't have a clear idea what happened to you.