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.