There's long been a dispute about whether religious freedom provisions limit the government's power related to religious sites on government land. These are usually American Indian sites, though in principle they might be other religious sites as well.
In Lyng v. Northwest Indian Cemetery Protective Ass'n (1988), the Court held that the Free Exercise Clause doesn't give religious groups the legal right to stop various government activities related to such sites (even though at the time, after Sherbert v. Verner but before Employment Division v. Smith, the Court had read the Free Exercise Clause as securing a presumptive right to religious exemptions from generally applicable government action). But one enduring question has been whether the Religious Freedom Restoration Act of 1993 should be read as perpetuating Lyng, alongside other Sherbert-era precedents, or should be read as superseding it. (See my Intermediate Questions of Religious Exemptions, pp. 652-56 for more on some related matters.)
In any event, this issue is now up before the Ninth Circuit en banc, which heard argument last week on it in Apache Stronghold v. U.S. (see, e.g., this Deseret News article [Kelsey Dallas]); the panel had ruled, 2-1, against the religious freedom claims, but the Ninth Circuit agreed to rehear the case en banc. My colleague Gene Schaerr at Schaerr | Jaffe LLP, at which I'm a part-part-part-time Academic Affiliate, represents the Jewish Coalition for Religious Liberty, the International Society for Krishna Consciousness, the Sikh Coalition, and Protect The 1st as amici in the case.
