It occasionally happens if you're rerouted involuntarily. The reason: with some airline computer systems it's easier to rebook you in the default fare class for your cabin rather than looking up your fare class and entering it. When an agent is trying to deal with a long line of angry pax from a cancelled flight, getting fare classes right is (correctly, IMHO) not his/her top priority. Of course, it's hard to plan for that - and not necessarily something you'd look forward to anyhow, unless getting miles is more important than getting to your destination on time. (This is the same reason people sometimes end up with class-of-service bonus when they're rerouted after upgrading a cheap ticket with an award or other upgrade credits.)