I've noticed that skulls and bones sometimes will not stack, because they are actually different, ie 'broad' skull, 'jawless' skull, etc.
And for some reason only some of those can be turned into bonedust. I always thought this was really weird considering the description of them says you can turn them into dust but figured maybe it was the description that was wrong and some types were for some other secret purpose.
I'm tempted to think its just a bug now though.