Congress also created the ATF to regulate firearms, but that hasn’t stopped states from banning weapons and magazines that are not banned by the ATF.
Also note that CAFE is a special case, because Congress specifically wrote a provision in the law that states were not allowed to set more stringent emission standards unless they obtained a waiver.
Anyway, states haven’t really had reason to ban certain medications before, because until now medications were relatively uncontroversial. There is only one example I’m aware of: Massachusetts tried to ban a new opiate in 2014. They were sued by the drug manufacturer, and the judge sided with Big Pharma to undo the ban.
Massachusetts did not appeal, so apparently all we have for now is two contradictory opinions by two lower courts. In other words, legally uncharted waters. While one can certainly hope that future rulings will undo the mifepristone ban, realistically most observers acknowledge that preemption is a complex issue and neither side is certain to prevail.