Contraptions and farms which use blocks in illegal positions (e.x. tnt duping) often break when the level.dat is forcefully changed. To reproduce this bug, one can: 

1. create a new world

2. set up a TNT duper

3. save the world and quit to the title screen

4. edit one aspect of the level.dat file (e.x. time)

5. reopen the world

 the tnt duper has updated and stopped working