When you take a mine cart ride and fall onto a mine cart track while flying over a solid block before said track (yet still landing on the track without touching the solid block ever) you will take fall damage later in the ride, often after you fall a distance again to another track (without touching solid blocks) or when you near the end of the current track. Evidence can be found in Hat Films' Epic Hatventure:

http://www.youtube.com/watch?v=1_xNbRppM48

It's been around since before 1.1. Similar bugs:

https://mojang.atlassian.net/browse/MC-363