I have a modified tree log automatic farm that is 13 blocks over the spawning dirt. It has one side where pistons are located to push the logs out of the spawning area. The problem is, the pistons are continuously replaced by wood blocks and thus the farm gets broken until the blocks are cut down and replaced.

tl;dr
1. Build automatic tree farm, more than 8 blocks high so large oaks spawn
2. use it normally
3. eventually, a tree branch will replace a piston or a tree leaf block will replace redstone
4. replace and repeat from step 2. it will happen again.

This happens with pistons, but i've seen it happen with stone/cobblestone too.
It was apparent on 1.6 but it got worse after i updated my world to 1.7, now it's a more common event.

This is probably the same issue as leaves replacing transparent blocks, but that bug is incomplete as it doesn't mention tree logs replacing other block types.