This has been an issue for a while, but I think this should just be fixed. The minecraft wiki had said it, and I've confirmed it myself by doing it:
(From http://www.minecraftwiki.net/wiki/Boat#Boat_physics)
"Boats do not break when running into Soul Sand at water level, because Soul Sand has a lower top surface so that the boat merely runs aground rather than crashing, so it is useful to make docks and harbors out of Soul Sand. Though Soul Sand now has the same bug as slabs, when you exit a boat while on Soul Sand, the player will take falling damage, usually enough to cause death."
I think that it would be much more efficient for the players who use boats to make these little harbors out of Soul Sand, and I think this minor soul sand with boat should be fixed.
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CubeTheThird
This is extremely easy to recreate, seeing as how it happens every single time. And it happens as soon as you run over the soul sand, not when you exit the boat. And it's not minor, seeing as how it INSTANTLY KILLS you. If it happens in Hardcore mode, that means you lose your world forever. And it's hard to avoid, because it also happens when you run over an animal. If you have a cat following you, and it falls far enough behind to teleport, it could teleport right underneath you, causing an unavoidable death.
What makes this even more aggravating is that this is a side effect of fixing the bug where boats protect you from fall damage. That exploit was extremely unlikely to ever be useful. I for one never used it because I have never been in a situation where it could be useful. Yet Notch considered it more important to fix that exploitable bug that doesn't matter than to fix this horrible bug that instantly kills you. They could fix this bug with no effort at all by simply bringing back the "no fall damage in boats" bug, and they SHOULD do that until they can figure out how to fix it without causing horrible bugs like this one.
Summarizing the "boats inflicts suffocation damage" to MC-881.
Can confirm. It is difficult to recreate though.