Villages are being generated in very buggy ways. Certain times the path is uneven, or the farms are 1 block above the path (meaning you can't get at them). Houses with doors 2 blocks up with no stairs beneath.
Found one on Seed 147896325 at x -247, z 325 that is a good example.
Villagers are also appearing 1 block lower than expected (ie within the path, but moving and not suffocating)
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As i've see this is a ongoing issue as I have seen this in multiple patches. (Likely terrain issue?)
The mobs falling through blocks problem is currently being tracked in MC-119 please only submit one bug per ticket.
While I agree the village spawning is messy, I believe that is as designed. Same thing with finding damaged end portals, missing villages due to chasm, etc.
I seriously doubt buildings the villagers can't enter is "as designed". It looks more like "tried to fix prior generation problems, and didn't quite get there".
also Chunk Errors are somewhat common in the latest snapshots in default with Villages it annoyes the crap out of me
the bug probably wouldnt be fixed without dropping frames on gameplay as villages trying to foucus on spawning on land can cause more lag and make a higher raritey for villages
but still they should still try to fix it
Yeah this problem seems to be widespread. I end up having to do a lot of fixing up any village I play in for any amount of time. It looks pretty shoddy, you would think they would want to fix this.

The reason for these problems is that the village structure component placing is somewhat simplified, I might call it a design bug. The reason why some houses are too low (doors buried) or farms too high is because their level is based on the average level where they are created.
While the edge of a farm could be too high on one side, it could be too low on the other side. Same for the houses. But overall they are at somewhat appropriate level for the area they are in.
Smartness into this would be to e.g. decide the level on buildings with doors (or other main entrances without doors) on that door spot (and one block out). For farms this is a bit more difficult as it does not have such specific obvious path point, but I think even they are created along paths in the village, so base on the side of the path.
The screenshot shows also buildings built on shallow water. This might be another issue, as the villages and villagers are not designed to work in water (e.g. in the code, villagers seem to avoid water...) The village (or at least parts of it) should not be there at all in the first place, or alternately, the villagers should move some extra dirt and gravel to make the area suitable for them (i.e. raise ground around the village's structures and paths).
What would perhaps be even easier, and actually emulate what happens in the real world, is to apply some landscaping around the buildings, either after placing them exactly as happens now, or as part of the placement process.

Landscaping is much more difficult than first sounds. Sure, it seems easy to dig away from dirt and grass (or add a little more), but then get into things like sand under rock and some trees on the other side... Removing sand but realizing to possibly leave the rock in place, or removing trees in a way to looks natural (i.e. not leaving leaves around, or not taking the leaves of the to-be-kept neighbor tree, or even giving that neighbor tree some extra leaves as it now has some empty space to fill...)
Just take a look how the simple lake generation routine fails with its landscaping (issue MC-610). Village landscaping would be couple order of magnitudes more complex.
There is a lot more issues along landscaping than those few mentioned above. Things that seem so trivial and obvious to us humans (like choosing in a split second that few blocks need to be removed or added) are sometimes near impossible for a piece of program. Or feel free to try and create an AI program with an eye to natural shapes, and which runs on average PC using less than 5% of its computing resources.
Additional complexity is that it would need to landscape the village even when it or its environment is not yet fully created - creating it chunk by chunk as the player moves... It would need to decide how to landscape around one house without knowing yet how the house just 16 blocks away is placed, or if there is a house at all but a ravine, or lake, or lava stream that will flow into the house soon after.
Perhaps so, I don't assume anything is simple without having been in the code. But I would also assume Mojang has some routines for some of those issues that they can reuse or adapt, and has perhaps solved some of them already since the conflicts generated villages have with the terrain are actually pretty mild compared to what they could be.
Well, considering that Strongholds are also poorly generated, I'd say that this is intended.
Also, this has occurred for a long time, since villages were introduced.

Yes, intended as in: done in a simple way since there is not more time to work on it and it shall do for now, players can at least work it out themselves. The better choice with some JIRAs for this kind of issue is "won't fix" with an explanation of the issue not being significant enough. Or not resolving it but leaving its fix in the "backlog", waiting for time to do it some unknown time in future.
This is not a programming bug, per se. More about design bug due to lack of development resources (i.e. time).
In 13w19a
This 'feature' makes villages a total eyesore! I saw villages spawn over ravines. It totally messes up the paths and the buildings spawn with a base that stretches to the bottom of the ravine. It's stupid how many villages spawn that are totally, unrealistically, messed up!

I've had that problem with village stairs & doors since their introduction. The very first thing I do when I encounter a village is in install all the missing stairs & doors. But I think the weird layout is part of the charm. You just need to play handyman to replace missing doors & steps.
This entry is reporting more than one bug. I'm not sure if it is valid.
I've realized something that could be fixed;when a village road generates in ground that is at level 63 then any village structures that are created by the road will have the entrance at a minimum of level 65 when it should be only one block higher,64.This causes the structures to be a block higher that they normally would be on any other road level.Under no circumstances can a village structure generate correctly when it is created by a Level 63 road*.So basically,just make the houses able to generate one block lower when the entrance is facing level 63 roads to fix this.This will not fix all village generation bugs but would make houses accessible from level 63 roads.
*exception:the extremely rare event that the block of road that the house entrance is connected to is at level 63 but there is a level 64 block right next to it and the house generates steps below the entrance due to it detecting a block there which would be a tall grass or flower block that had not disappeared when the gravel generated under it.
This only happens under non-superflat world generation. This bug can occur in all three gamemodes, not just survival.
I can cope with untidy villages. The only real problem is houses that suddenly go up/down one level halfway through, so the ceilings and floors don't match up.

@Kevin: I think the problem you are describing might have something to do with MC-7294. If you do catch more of those level shifts, please add more cases to that one, as I haven't seen any other cases of it yet. Makes hard to catch the bug, or even to know if it still exists.
@Markku
I agree that MC-7294 is probably a major cause for this issue.
MC-31380 is an example of how villages that are naturally generated are useless to villagers commonly.
It surely doesn't help that both plains and deserts have gotten much hillier over the last few versions. It might help if village generation had some capacity to kick back against terrain generation – perhaps modifying things along the lines of "there was a hill/lake/cave here, but the villagers leveled/filled/sealed it".

@David Harmon
Many a problem could be solved easily, if the whole village and its terrain was known before any part of it was laid down. Alas, villagers are created just like the terrain, chunk by chunk, so when one chunk would need to know e.g. how the area was flattened by the villagers, there just isn't enough info available (the rest of the nearby terrain might not exist yet). Brute force solution is to load more chunks temporarily, but this leads to other problems, especially with non-3D chunks as minecraft currently has.
Though I've already covered that and some more in an earlier comment.
I started MC-45682 a few days back and was eventually lead here and my guess on what's going on is that the generator doesn't handle uneven terrains and villages very well. I don't know how the code behind this is set up but is it possible to put a check for blocked doors or some of the glitches...then again thats probably a huge block of code just to do that.
Ps: MC-45682 can be marked as a dup of this one, they are part of the same problem
Ok..just came accost a good example world for this seed, and its definitely still active in 1.7.5: 4981279424677297828
coordinates:
x = -170
z = 110
the entire village is literally 2 blocks higher then the surrounding ground even though its on almost level ground
also will be Generatet Gras under Village- Houses
Confirmed in 1.8-pre2

From MC-87586: Seed 1280411122, Coordinates -180 70 610

I'm relatively sure I can confirm for 16w21a for the village example in MC-102103.
Why is this marked as working as intended? I see no comment explaining it.
Because @unknown said so.