the federal government merely tolerates the semi-autonomous nature of states in order to maintain order. but the legality of the federal government's supremacy is well evolved, its power and might is extremely disproportionally higher than any collective of states, and at this point the semi-autonomous nature of states is pure fiction as the federal government can assume jurisdiction over any intra-state matter if it wanted to through its interstate commerce laws.
yes, federal level law enforcement can theoretically charge someone in a cannabis-legal state for drug offenses. this still happens. the discretion of the words of the President, the heads of the DEA and DOJ prevent the MAJORITY of it from happening and also guide the discretion of the courts and public sympathy. so right now, for the last two administrations it has not been a priority to upset the social order in cannabis-legal states. but it can still happen.