Repurpose the waste from the imprecise assembly of machines for new materials. No process is ever truly perfect.
Mods introducing new content into the game.
New Ores and resources as well as machines.
Furnaces, assembling machines, production chains.
nuclear science also produces scrap, which shouldn't? https://mods.factorio.com/mod/atan-nuclear-science
As of 0.9.3 this issue should be fixed.