I am having the same issue. It has affected villagers, pigs, and cows. It seems to happen when a mob is stuck inside of a wall. I traveled to the locations of two errors I had seen, and the coords listed in the last part of the error (1='World', X=# Z=# Y=#) were inside of a block. I think it is happening when a mob glitches inside of a solid block. (The ones I investigated were stone and a log, both opaque).
When a mob despawns, I get this message in console:
[13:11:30] [Server thread/WARN]: Wrong location! (5, -40) should be (5, -41), acf['Sheep'/435295, l='Snapshot World', x=88.31, y=65.00, z=-635.11]
Edit: this error was seen in Snapshot 14w30c
I am having the same issue. It has affected villagers, pigs, and cows. It seems to happen when a mob is stuck inside of a wall. I traveled to the locations of two errors I had seen, and the coords listed in the last part of the error (1='World', X=# Z=# Y=#) were inside of a block. I think it is happening when a mob glitches inside of a solid block. (The ones I investigated were stone and a log, both opaque).
It should be possible to "repair" a partially-generated portal with eyes of ender. For example, a single piece of portal frame may be able to generate the rest of the portal structure if it detects that it is missing. When you put an eye of ender in it, if it detects that the other needed pieces of portal frame are missing, it will generate the rest of them over the lava pool (to keep it centered). This could be expanded upon by making another part of the stronghold be able to generate another entire portal room in case that whole thing gets generated over. Alternatively, strongholds could generate last, and cut into ravines, mineshafts, etc if needed.
If you have an Nvidia GPU, this can be caused by setting image settings to "Use advanced 3D image settings". To solve, go to your Nvidia Control Panel and go to 3D settings > Adjust image settings with preview and select "Let the 3D application decide". This will not solve issues on non-Nvidia graphics cards.
I have reproduced this bug in 14w29a. The bug happens as described.
I have noticed this a few times on my computer. It seems to happen more frequently when the game is maximized while lagging, such as when first opening the world on a slower computer or if there are a lot of entities. As a temporary work around, this can be fixed by setting the game to not fullscreen and back to full screen. I have also noticed that this happens when switching from non-maximized mode to maximized mode while lagging. I have not noticed this on any of the new snapshots and I have not tested for it in 1.8-pre1, but this affected 1.7.10 and earlier versions.