I got pinched by the fare bucketing recently. I was traveling with someone else on two separate flex reservations, and we decided to take the earlier train, which was the same fare. I changed my ticket, but when I went to change their ticket, it wouldn't let me. Seemingly what happened is me moving to the earlier train must have gobbled up the last low-fare ticket, so it wouldn't let them move to it. Of course Amtrak's ridiculous website just threw an error when trying to do it until eventually after an hour it showed the new fare.

To add insult to injury the price on the original train had jumped too, so moving back to it wasn't easy, either! Fortunately it dropped back down and I was able to at least have us both on the same train again.