Some crafting machines give obsidian but it doesn't immediately show up in inventory (see attached picture).
Sometimes you can make them visible using alchemy terminal (seems to force refresh), but not always. So, I'm not sure what's exactly the problem there.
It's no big deal, this stuff eventually reappears but it can be kinda annoying when u find out your obsidian reappeared when you are in Outlaws, for example...