When teleporting into an unloaded chunk in 1.8, the player would fall while the chunk was loading, but be teleported back up by the game when the chunk loaded. This is not the case in the 1.9 snapshots.
To reproduce:
1) check your Y coordinate
2) while not flying, type this command: tp ~1000 ~ ~
3) as the chunk loads, you will fall down
I expected to be teleported to my original Y coordinate like in 1.8.
Instead I spawned in the stone under the surface and suffocated.
This is much easier to reproduce on a server with high ping.
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Can anyone else reproduce this?

No, that's not a dupe of that bug!

To reproduce:
1) check your y coordinate
2) while not flying, type this command: tp ~1000 ~ ~
3) as the chunk loads, you will fall down
I expected to be teleported to my original y coord like in 1.8 but instead I spawned in the stone under the surface.

Confirmed.

I'd like to confirm this and provide a little more detail. Since the 1.9 update, many of my teleport commands (mainly command blocks) are teleporting players to coordinates that are 2-4 blocks lower than the command parameter. Repeated tests reveal the players fall after teleporting, which is what causes the drop.
The attached screenshots are from a teleporter that I had just set up; prior to taking the screenshots, it was putting me 2 below instead of 3. Old teleporters also exhibit this behavior, but not all of them. The behavior can occur no matter where the target is, but it seems more likely to occur on chunk boundaries. The distance below the surface seems directly related to how long it takes chunks to load.

One thing I forgot to mention: If a player teleports and falls but doesn't fall enough to suffocate, they instead get stuck bouncing up and down until I teleport them again.

What versions can you confirm this for?

I've witnessed it in 1.9 and 1.9.2. We never saw the bug before then.

I can also confirm with version 1.9.
Using the /tp command to teleport to random x and z coordinates to locations that have not yet had their chunks created can occasionally make the player "fall", and the ending Y coordinate ends up being less than the Y provided in the teleport command, often placing the player underground and causing suffocation. Through my testing, this only occurs when teleporting to chunks that have not been created (as opposed to not loaded), though more testing may need done to see for sure.

I can confirm through the repeated experiences of players on my server that this problem does occur for existing chunks. That's pretty much the problem for us: We have teleporters (command blocks) to get to certain locations, and those teleporters are now killing players by suffocation after falling.

Can anyone confirm for the 1.9.3 snapshots?

@Jason this has happened to me when teleporting into my base, so the chunks have definitely been loaded (we were trying to set up a TPer system to replace the broken portals at the time).

FIxed by 1.9.3 pre-2; now teleports you back up as in 1.8.

@L M What version are you running?

Not fixed in 1.9.3 pre-2 and pre-3, just harder to reproduce.

just harder to reproduce
Mind sharing the "harder to reproduce" steps then?

Oh I was testing MC-89928 which involved teleporting to specific coords and kept ending up 5 or so blocks below my target. I was teleporting to underground locations while in creative but I would type, say, "/tp 6400 35 64" but fall to (6400, 31, 64) before or as the chunks loaded. To reproduce, perhaps try teleporting to a target location which is already underground, or being in creative? I'm guessing that, similarly to MC-89928 and MC-98153, server load increases the chance of this issue occuring as well as its severity as the chunks take longer to load.

Cannot confirm for 1.10.2. I find I am teleported back up once the chunk has loaded.