@RingoStarrDrums Her Majesty  was originally intended to be a part of the Medley, sitting between Mean Mr. Mustard and Polythene Pam . When they put together the first rough mix of the Medley, Paul listened back to it and decided it didn't fit, so told the engineer to cut it out and throw it away.

EMI had given that nothing was ever to be "thrown away", and so as soon as Paul left, the engineer picked it up off the floor, added about 20 seconds of leader (blank) tape to the end of the Medley, and then stuck Her Majesty  onto the tape, to ensure it was preserved.

The next day Paul had an acetate of the rough mix of the Medley cut so he could listen at leisure. The record cutter who made the acetate did an exact copy of the rough mix tape that he'd been given, including the silence and Her Majesty , assuming that was what was wanted.

When Paul listened to it later, not expecting to hear Her Majesty , he was pleasantly surprised to find it there, at the end. It amused him. He liked it. And so that was where it ended up. What you hear is exactly what was chopped out of that first rough mix of the Medley. The crashing guitar chord at the beginning is the end of Mean Mr. Mustard, the clipped ending is because part of the last note remained in the rough mix of the Medley because they were not looking to be precise, it was only a rough mix.

So, we end up with Her Majesty  becoming one of the first (if not the first) hidden tracks on an album (while it is on the tracklisting now, it wasn't at the time, no mention of it at all on the record sleeve, making it as big a surprise for listeners then as it was for Paul when he first heard it there).

The Beatles liked to capitalise on accidents, and this was one such incident.