Sometimes Air Blocks are generated inside huge Water Bodies. Often appearing in Groups of two or three.
Example Location
Seed: 292202
Coords: -472;54;69
Related issues
is duplicated by
relates to
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Can confirm this, though don't have a seed handy to show it. Can you supply seed and coordinates of above screenshot Kevin?
You can find these very close to spawn.
Seed: 292202
Coords: -472;54;69
Given Location is the center of four of these Air Pockets
Bug is reproduceable: same seed, same location, same problem.
note: My Client is pure Vanilla
Confirmed here with that seed/coordinates.
Still appears on 1.4.4 (same Location and seed can be used).
Case Updated to reflect new version
Added Coords and Seed in Description
Changed Gamemode to "none" since it appears on all Modes.
Still appears in 1.4.7, same seed, same location

This is a bug in creation of mineshaft "rooms" or the connections of corridors to a room. Digging deeper... I mean, analysing the source code.
I had this happen while going to the end of the World of Minecraft! In the Water, I saw these!

Found the bug, and fixed it.
There is a piece of code that offsets a generated structure (including its substructures) in vertical direction, e.g. moving mines downwards. Unfortunately, bad design raises its ugly head again; that method doing the moving does it completely by itself, instead of requesting the structure parts to do it to themselves.
In this particular case, mine rooms have additional internal data that would also need to be shifted. As they are not shifted, they remain at the nominal height (50-some), and end up being carved somewhere above, in this visible case from the water of oceans. (There are probably many such empty volumes inside ground, too).
Fix
These changes will move the air boxes down into the mineshaft rooms where they belong, thus correcting the water (this issue), and also actually doing what they were supposed to do - making sure the main corridors have clear connections (instead of having e.g. their tops blocked by stone).
StructureStart
protected void markAvailableHeight(World world, Random random, int offsetDown) {
...
int vertical = structureHeight - this.boundingBox.maxY;
//this.boundingBox.offset(0, bottom, 0); // BAD
this.offset(0, vertical, 0); // FIX FOR FUTURE (not this particular issue)
Iterator var7 = this.components.iterator();
while (var7.hasNext()) {
StructureComponent var8 = (StructureComponent) var7.next();
//var8.getBoundingBox().offset(0, bottom, 0); // BAD
var8.offset(0, vertical, 0); // FIX
}
}
/**
* <p>Default implementation, let more complex start components override this.</p>
*/
public void offset(int x, int y, int z) {
this.boundingBox.offset(x, y, z);
}
StructureComponent
/**
* <p>Default implementation, let more complex components override this.</p>
*/
public void offset(int x, int y, int z) {
this.boundingBox.offset(x, y, z);
}
ComponentMineShaftRoom
public void offset(int x, int y, int z) {
this.boundingBox.offset(x, y, z);
Iterator linkedComponentsIterator = this.boundingBoxesLinkedToTheRoom.iterator();
while (linkedComponentsIterator.hasNext()) {
StructureBoundingBox bb = (StructureBoundingBox) linkedComponentsIterator.next();
bb.offset(x, y, z);
}
}
Above changes are tested on top of 1.4.7. Clear waters, nice open passages from the start room.
NOTE: there may still be other effects causing empty spaces in water, but at least on couple maps I checked quickly, this reason is either the majority or only reason.

Affects 13w09b.
Updated this issue; Still present in 1.5
updated this issue, still present in 1.6.1

Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

Still there in 1.6.2
Confirmed in the 13w36a
Confirmed in the 13w36b
Confirmed in 13w37b

Confirmed in 13w41b. Just encountered several.
I've seen them in 1.7.1
Evidence that it is indeed in 1.7.2
http://imgur.com/7aOciwe
😞
Someone just posted this on reddit: http://www.reddit.com/r/Minecraft/comments/1pc2jn/how_to_easily_find_mineshaft_in_deep_oceans_using/
Apparently these bubbles are created when mineshaft dirt rooms are generated. That should probably help in fixing the bug.

@moderators could you perhaps add a link to the earlier fix-comment to the issue description, so others can notice it.
@redstonehelper
If you take a look at the earlier comments, you'll find the same results and the fix already there. Been there since 19 Jan.
@Markku Oh, damn, I forgot to check older, hidden comments. Sorry!
I got the same problem, but not in an ocean
More screenshots for good measure.
Still present in 1.7.4
Still in 14w04a :
seed 1082326624105029725
positions: X=34, y=58 z=-2356
X=-275 Y=74 Z=-2357
Confirmed
Still in 08a (see MC-49299)
I just found this in my new survival world on 1.7.5. (Seed: 1051732723, South/West of spawn island.) There is gravel at the seabed with mineshaft tunnels right below that.
When I was exploring the mineshaft I found that the roof was mostly gravel so maybe that has something to do with it.
Images:
http://imgur.com/ELRAOtF
http://imgur.com/myEC1o6
http://imgur.com/w0DFXgf
http://imgur.com/hnULgJy
http://imgur.com/HKnVkDj

The materials (e.g. gravel) have nothing to do with it. The reason has been figured out and an example code fix given more than a year ago (buried in the older comments). All we're now doing are confirming occasionally that Mojang still hasn't fixed the issue and providing new seeds/examples (as world generation changes and old examples become less useful).
(Those gravel/sand ceiling tunnels do, or at least did, have their own water issues, but its not this one.)
still here in 14w11b
14w17a too
and 14w18a

Confirmed for 14w21b
Confirmed for 14w25a
I have the feeling the amount of air pockets has increased since the snapshot 14w25a, I have never seen any and now they appear pretty regularily. Might have something to do with the spawning of water dungeons.

Confirmed for 14w28b
and for 14w30b
Found some in 14w31a.
14w33a.

Still present in 1.8-pre2
Seed: 35267400
Coords: 1862, 64, 328
still present in 1.8
reason/fix has been given by Markku already...
Still in 1.8.1-pre3.
Damn, I'm sorry to see this "bug" go, these are actually USEFUL — they mark mineshaft central chunks! Seriously... dig straight down from one of these air bubbles, and you'll find a mineshaft. Every time.
Wow! You're the first person to ever realize this!
I wonder if there's a way to "un-resolve" this, as it's a nice marker. But, like glass towers marking the strongholds in ancient versions (like pre-alpha or indev, I think)... I think we're out of luck.

This was a clear bug (not just a "bug" in quotes), and the locations of the center rooms were never meant to be detectable from above in any way, let alone in such a silly way. (Mine structures in general can be considered to be only detectable when they carve through into open space/water or just below sand layer and the sand falls down.) The bug's result was useful in a way as in any bug that can be abused is; e.g. collision bugs used to shoot or move through walls, duplication bugs used to get "infinite" items, etc. (There are bugs that are useful without being considered cheating, e.g. redstone implementation bugs that allows making BUDs, but even those should be solved by implementing a proper BUD item and fixing the implementation. But that is worthy of its own long story in forums instead of here.)
If one wants to cheat and find the center rooms easily (nothing wrong in that, as long as you do it in a single-player game, or if accepted together in multi-player), a mapping program will do the trick. Then one doesn't even have to actually look for those somewhat difficult to see air bubbles (and impossible to see when they are not below ocean).
And we're not out of luck. Considering the history of bug fixing for Minecraft, it was actually pretty darn lucky that this bug was (eventually) fixed. Now, if we could get a few hundred more cases of being as lucky...
"Pocket" shouldn't have been removed from the labels because it refers to air pockets, not the Pocket Edition.

@unknown, that was intentional
@unknown But what if someone searches for "air pocket" and doesn't find this report?

I guess the label bubble
is as wrong as Pocket
as bubbles are rather the air bubbles particle underwater
However when you use the search bar, it searches in the simply mode for the text
element, which is the same like searching in advanced mode for
text ~ "\"Pocket\" shouldn't have been removed from the labels because it refers to air pockets, not the Pocket Edition."
Which leads to this report
Guys this bug is back in 16w06a. I am seeing it right next to an ocean monument. So much so that guardians have fallen into and are flopping around. I can show screen shot if needed.
Please provide seed and coordinates if the issue persists in worlds generated in 16w06a.