This is not an easily noticed bug but if you can get to a rare structure within a few minutes of it loading into a new chunk you will find that the loot chest(s) has items scattered around it making it possible to gain more loot than you should.
Looking into this further (using MCP to print messages to the console) it appears that the structures spawn on top of eachother 4 times, each time breaking and replacing the chests. An easier way to reproduce this is to find a rare structure such as pyramid in singleplayer then close the world and delete the region folder before regenerating the map's terrain.
Could not reproduce easily in 1.4.7, but I only tried with one desert temple in one world, multiple approaches (teleport on top vs. fly into the region), each approach on a new instance of the world.
Source code has two different checks to avoid regenerating chests.
The situation must be quite special to bypass the checks. Steps and world seed+location to reproduce would be nice (and without messing with the world save, but instead just recreating the world).