Major You can't eject certain items from manufacturers.

[kyle2143]

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.