This is pretty rare i'd say. If your BP somehow failed to scan properly, then you were not registered on the manifest. Also from a security standpoint that's a pretty big f**** up!
You may very well have problems getting the miles/XPs. Depending on how they fixed it: If they marked your flight as Flown you should be able to retro-claim. If they simply reinstated the canceled flight I'd say it would be very very difficult to get the flight credited..