What are some cases when the federal government went against a state law that people voted for in that state?

Abortion was legal in Colorado, but was illegal at the federal level. Same with civil rights laws. Amazingly though, 0bama is the only goof I can recall who actively battled a state (US v AZ) to stop them from protecting their own population!

Tyrannies tend to fight local gov't. I'd expect more of these actions.

Checks and balances apply to all parts of the government: the Executive, the Legislative, the Judicial and the people. If the constitutionality of the laws passed by Congress or passed by the state legislatures can be challenged in court, why do you think the constitutionality of the laws passed by initiative or referendum can't also be challenged? Of course they can. There's nothing in our documents or in our legal and political traditions that declares laws passed by the voters as holy, sacred and not liable to court tests of their constitutionality.

Literally, hundreds of voter-passed laws have been been challenged and quiet a few - either whole or in part - have been found wanting either because they didn't conform to state law or to federal law or to the constitutional provisions contained in the Bill of Rights or the other amendments.

Google State Iniatives Overturned By The Courts for some links.

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Arizona immigration enforcement.

Gay marriage, right to die in Oregon, Arizona's illegal immigration law.

California's medicinal marijuana law.

Gay marriages