Josh: Had this issue occure twice now. The first was with the Wither Arena where it recognised I had 3 Wither Skulls, but only took 2, leaving 1 that wouldn't stack with the others. Now I'm having it with creeper skulls. Just got 2 from killing mobs, they wouldn't stack with each other, and only 1 would sell. I've placed the other and broken it (advised by wakka during the wither issue), but that didn't fix it.