Part of the problem is that Eureka Moly stated they do not intend to permanently occupy the land (dump site) since their mining will end in 40 years but they presented no plan or intention of removing the dumped waste rock from BLM land. In essence insinuating the the waste rock and any of the contaminates it may include, would be BLM’s problem after 40 years.
I have worked on several mine waste dumps and they can cause big problems later on depending on the minerals contained within them. Certain minerals once exposed to air can oxidize and degrade into some pretty nasty stuff that pollutes the land and ground water. Eureka Moly seems to have no other plan for their mine waste other than to dump it on land they do not own and just leave it there.
I don't know the specifics of mining molybdenum, but tailings, waste water, and site remediation have very long-standing and detailed regulations and rules from BLM/Interior and EPA. I doubt that any government agency would allow them to "just dump it."
Rather, it seems to me the judge is completely re-imagining 150 years of precedent, law and practice, for what I suspect are purely ideological reasons.