All I've done was change the height of the stone layer from 59 to 5 in the "Overworld" preset when customizing the Superflat world type.
This had led to Abandoned Mineshafts and fragments of a Stronghold to spawn in mid-air, high above the ground. Apparently the Mineshafts are allowed to do that, but I haven't found anything on Strongholds, which also only spawn partially, without being connected - check the screenshots included.
The word seed is: 360212915417252929.
Is this still an issue in the current Minecraft Snapshot 15w47c or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.