If the item selected to eject in the manufacturer menu is not a standard material, then the item cannot be removed from the manufacturer ever. They can be used to manufacturer things I think, but you can never get back the block you put in. Well, not without destroying the manufacturer.
This is really only and issue for miners since sometimes a miner will set the output of the nano-forge to the mining manufacturer. And you'll basically be putting blocks of emerald or lapus lazuli into the trash, never to see them again.
I heard someone mention this and say that its actually crystalline matter, turned into the blocks, that have this problem.
I put a few blocks of synthrubber and copper bars in one and I could definately take the synthrubber back out. Not sure about the copper.
Can confirm this, and it doesn't only apply to crystalline matter, I had it happen with bee wool in a robotics manufacturer. I dont know if somewhat related, but if you put the material processor's output to the mining fabricator, it puts in the bars, but displays only 10 units, if you take out 1 unit, it dispenses all of the stored units of that type, so the items dont actually disappear. And robotics manufacturers use pharosium when the recipe needs metal, so it quickly runs out of conductive metal, it should use steel, then mauxite, then pharosium to conserve materials.
this bug is now fixed and it was the stupidest possible reason
it was checking the material's internal id against the material's name, so anything that had it different -- like "(adjective) diamond gem" -- wouldn't match and wouldn't be able to be ejected