They're so concerned about getting stuff for free, they don't care about following the law.
If the ACA has any reference to the "Federal Government" as being separate from the "State", then HHS loses on the basis that the statute makes the distinction. Had they read it first instead of "passing it to find out what is in it", they may have foreseen some of these challenges.
Of course, this logic doesn't prevent Roberts from taking off the robe and putting on a Congressman hat again...