Similar bug with the nether fortress generation concerning the obsidian pillar in the End.

(https://mojang.atlassian.net/browse/MC-5870)
Some parts of it spawned invisible und when you try to walk on them they "trap" you. You are unable to move and shake.

When you destroy the vrystal, it disappear and sometime the pillar half-appear (screenshoot 2013-01-15_17.56.42), other time it disappear too.