Hopper-hopper duplication
This is a really serious duplication bug.
To reproduce:
1). Place two hoppers facing each other.
2). Place one item in one of them.
3). Go away 200-250 blocks and stay afk for several hours. The longer you stay the more items it will duplicate.
I found this bug while using Etho's hopper-hopper timers with dirt (http://youtu.be/bYwzd62cLSw). Duplicated dirt made the system turn off.
I haven't tested this in a brand new world, but it works in our survival server for sure.