Something like what you describe only happened to me once, and that was at the gate, not in advance. I was traveling with my wife and we got separated as a result. Never got an explanation and when I asked the person in my former seat when and how she was assigned that seat she wouldn't talk or even look up at me. I suspected she was an air marshal.

Then there was this oddball, where the entire plane got reseated: Bizarre seat reshuffle

Finally, seat changes can also happen for "schedule changes" that aren't really schedule changes. They change the flight number or go from, say, an E170 to an E175. Little or nothing really changed but the system can't preserve the seating even when it should have been simple to do so.