Bones, Rotten Flesh, Gunpowder, etc. are hard coded into the mob's drop rate and you cannot prevent them except by running entity detecting command blocks, but typically that's way too much effort.
I played through the map without making a grinder and still got all the normal drops. The fact that there is a junk trader for rotten flesh proves that this functionality is intended.
This is no longer the case in version 1.0 of the map.