Justice Sonia Sotomayor (joined by Justices Ginsberg and Kagan), is upset with the rest of the rest of the Supreme Court:
Those who are bound by our decisions usually believe they can take us at our word. Not so today. . . That action evinces disregard for even the newest of this Court’s precedents and undermines confidence in this institution.
The context of this bellyache is an injunction issued by the Supreme Court barring the enforcement of the Obama administration’s birth control mandate against Wheaton College. Myriad religious organizations, including Wheaton, complained that complying would violate their religious beliefs. The administration then responded with a bogus “accommodation”, wherein the organizations would file a form objecting to the mandate, at which point pretty much the same thing would happen: the health insurer would issue a separate policy just for birth control, and pass the cost on to the organization. The various religious organizations weren’t fooled by this legerdemain.
The basis for Sotomayor’s complaint was a section in the majority opinion in the Hobby Lobby case that read:
In fact, HHS has already devised and implemented a system that seeks to respect the religious liberty of religious nonprofit corporations while ensuring [blah blah blah]. . . We therefore conclude that this system constitutes an alternative that achieves all of the Government’s aims while providing greater respect for religious liberty.
Thus, Sotomayor, et al. complain, the majority already approved the “accommodation” and are now going back on it. But they are not.
Under the RFRA, the government cannot burden religious freedom unless it is the least restrictive means to accomplish a compelling state interest. Nothing here says that the accommodation is the least restrictive means. To the contrary, it says only that the accommodation is a less restrictive means than the mandate that the administration sought to impose on Hobby Lobby, and therefore the mandate cannot be the least restrictive means. (ASIDE: The majority opinion also never found that free birth control was a compelling state interest, either.)
It’s sad that three Supreme Court justices don’t understand the basic logical distinction between “less” and “least”.
TANGENTIAL POSTSCRIPT: However, if you want an example of the Supreme Court going back on its word, there’s New Haven v. Briscoe from 2012. In that case, Supreme Court waffling left the hapless city of New Haven with no way to follow the law. In 2009, the city set aside the results of a firefighters test because no black applicants passed the test and they were afraid of a discrimination lawsuit on the basis of disparate impact (the theory wherein you can find racial discrimination based purely on numbers, without any evidence of actual discriminatory policy or conduct). The Supreme Court said they were wrong to set aside the test, adding:
If, after it certifies the results, the City faces a disparate-impact suit, then in light of our holding today it should be clear that the City would avoid disparate-impact liability based on the strong basis in evidence that, had it not certified the results, it would have been subject to disparate–treatment liability.
This certainly sounds like the Court saying that New Haven was safe from a disparate impact suit. But when such a such a suit duly appeared, the lower court found for the plaintiff, and the Supreme Court wouldn’t even grant cert. The city, quite literally, was sued successfully for obeying the Supreme Court.
Strangely, I don’t remember a strongly worded dissent in that case.
Internet Scofflaw 
What she’s seized on here isn’t so much a matter of law as a public relations issue for SCOTUS. Alito’s inability or unwillingness to own the breadth of yesterday’s decision is feeding into the public perception that the Court is engaging in a sleight of hand. And perhaps it did.
They still have yet to fully engage with the “substantial burden” question, which in my opinion is a far more interesting and pertinent issue than least restrictive means in the Wheaton College case. The form is clearly not the “least restrictive means” of accomplishing birth control coverage if it doesn’t, as the government concedes, actually trigger coverage. But is it a “substantial” burden upon the exercise of religion? I’m skeptical, but Hobby Lobby didn’t give us much guidance.
Any breadth came from the RFRA itself, which pretty much dictated the result. As far as the “substantial burden” question I find it remarkable that anyone would suggest that ordering them to pay personally (Hobby Lobby self-insured after all) for abortion drugs might not be a substantial burden. Megan McArdle put it well: