Added two screenshots about the problem with strongholds
@Anon Ymus
The stone blocks which are visible at the right of the first screenshot
Since reloading the world solves the problem I don't think it could help. At the beginning right after the bug I tried looking in a external viewer such as minecraft X-Ray and it showed the world normally.
In fact it IS the MC-5737 bug as seen with the village not generating correctly, as if the "stone chunk" was part of the non structured building chunks (EDIT: saw the mail of duplicate flag for this JIRA)
I'm with the latest snapshot (13w19a).
I entered in the nether and I saw Zombie Pigmen not having swords and directly attacking me without provocation from myself. I went further and then I saw "normal" zombie pigmen having a sword and being passive.