I've seen it a few times years long ago when the scanner was down, or power to the gate was down after a storm. GA's pulled the stub and input them later (obviously dating the timeline when this happened).

Here is where the stories diverge. The guy in Houston boarded a row at a time from the back and looked at every boarding pass. It went OK. Flew there a lot back then. Happened to me at least twice.

The time it happened in Kansas City was far goofier. Three very delayed MD-80's with full loads quickly being hurried out after weather cleared while the crews were still on the clock. They had even borrowed planes from the old TWA maintenance hanger. There must have been rebooks and seat changes nobody could see or even new about. A couple of poor women started loading manually by group without checking seats off as they went. A large seat dupe festival quickly developed. As I remember they tried to figure it out, then decided they didn't have time to, and just gave up when every seat was full, closed the door, and started on the next plane.