The nether ruined portals, supposed to spawn across the surface made their way into deep caves. This might not be a bug, but to my knowledge, before 12w08a, these structures would naturally spawn either in oceans or the surface. But now, however, they can spawn like the geodes, underground, even at deep depths, as proven by the photo accompanying the report.
Linked issues
is duplicated by 16
MC-274953
Ruined portal generated in the overworld river will fail, and the ruined portal will be generated underground (y<0)
Resolved
MC-276741
Ruined portals Generate underground
Resolved
MC-278799
Nether portal generation underground
Resolved
MC-242495
Ruined Portal carves out a really wierd looking cube around it.
Resolved
MC-241404
buried ruined portal
Resolved
11 more links
in previous versions ruined portals could spawn underground and did, though infrequently. this seems like WAI to me.