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The Supreme Court added to the complexity last year when it upheld the core of the law but said states should be allowed to opt out of the Medicaid expansion. Some statehouses are still grappling with whether to accept the opt-out.

Meanwhile, on Capitol Hill, lawmakers have gone back and recaptured some of the money the law would have overpaid as tax credits for those using subsidies to buy insurance on the exchanges.

And all sides agreed in 2011 to repeal a business expense reporting requirement that had been designed so the IRS could make sure employers were paying their full tax burdens.

This week’s decision signaled that more tweaks and changes may be on the way.

“These things have never been that easy,” Mr. Jost said. “I just think it’s so unfortunate that it’s turned out this way.”