As stated in the National Review report, Judge Collyer doesn't have the final say on this issue and her ruling may eventually be overturned by the court of appeals or Supreme Court.

Obamacare Lawsuit: House Republicans Win a Round Against the Obama Administration
David French | National Review
May 12, 2016
http://bit.ly/1XntupK

[snip]

Federal district court judge Rosemary Collyer ruled today for the House of Representatives and against the Obama administration — holding that the administration unlawfully spent money that Congress did not appropriate for the sake of propping up a key Obamacare subsidy.

At issue was Section 1402 of the Affordable Care Act, a provision that required insurers to reduce deductibles, copayments, and other cost-sharing mechanisms for lower-income Americans sand provided for government subsidies to make up the insurer’s losses. But while Congress passed Section 1402, it did not subsequently fund the government subsidies. Indeed, President Obama signed into law both a continuing resolution and a consolidated appropriations act that did not fund Section 1402 payments. His administration made the payments anyway, and the House sued.

The court’s reasoning was simple. Constitutionally, the executive branch simply doesn’t have the power to spend money that Congress hasn’t appropriated.