Just to be clear: When you say "separation of powers", it means powers of the various branches of the Federal government. That is, the powers of the Executive branch vs the powers of the Legislative branch vs the powers of the Judicial branch.
When you say "states rights", you mean the powers of the states vs the powers of the Federal government, which ever branch of the Federal government might be involved in the specific case.
So, do you mean states rights vs Federal rights issues, or "separation of powers" issues? The two sometimes get confused.