Under the supremacy clause, federal law trumps that of states. States can't nullify federal law, either; there was an issue with that, too. I don't know that I agree with the precedent on this absolutely, and it might be less of a problem to start with if the feds passed very few stupid laws, but that's how it stands today. By your logic, a state can override the civil rights act of 1964.
It’s not something subject to a court. The FBI could haul in a user of state-legal marijuana and charge them with crimes in Federal court whenever they want (subject to the federal law prohibiting funds being spent on prosecution of medical marijuana in certain states).
That it isn’t happening regularly is just because the FBI/DEA and other federal agencies aren’t currently focused on it. That could change any time at the whim of an executive order from Trump.
