A federal judge struck a blow to the Biden administration’s antitrust agenda last week, ruling against the Department of Justice’s effort to block a merger between two of the nation’s largest sugar producers. Yet for members of the administration who had spent months following the case, the outcome of the ruling wasn’t the only thing that frustrated them. It was the way it came about.

Barbara Fesco, the U.S. Department of Agriculture’s top analyst of the sugar industry, was a key witness in the case, in which a $315 million deal hangs in the balance. The Justice Department had argued that the transaction would lead to higher prices for millions of Americans as an already concentrated market underwent further consolidation, leaving just two companies in control of roughly 75% of all sugar sales in the southeastern United States.

Fesco, however, argued the opposite.

Appearing before the court as a witness for U.S. Sugar, Fesco told U.S. District Judge Maryellen Noreika she believed the company’s acquisition of Imperial Sugar would ultimately benefit consumers. Her assessment, she went on, was based in part on her relationships with executives at the companies involved, who had assured her they had no plans to raise prices. “Knowing these people as long as I have,” she said, according to a transcript of her testimony, “I had high faith that it was good.”

When asked if she had seen any data that supported her belief that the merger wouldn’t lead to higher sugar prices, Fesco said she had not.

Her testimony was enough to help convince the judge that the deal should be allowed to go through. On Sept. 23, Noreika, who was appointed by former President Donald Trump, ruled against the Biden administration, citing Fesco’s testimony prominently as evidence that the merger would not violate American antitrust law.

The Justice Department quickly appealed the ruling, and the incident left officials bitter over a government bureaucrat who had worked against the interests of the administration under which she serves.

“It is extremely disappointing to see a member of the administration undermine the enforcement work of another agency and the broader goals of this government,” an administration official who requested anonymity because they were not authorized to speak on the matter tells TIME.

The case has flipped the normal positions espoused by Democrats and Republicans when it comes to the duties of regulators within the executive branch. Typically, it is Democrats who defend the independence of government bureaucrats against the agendas of political appointees. Republicans often argue that regulators should comply with political leaders under a conservative governing approach known as the “unitary executive theory.”

The USDA did not respond to multiple requests for comment. Efforts to reach Fesco directly were unsuccessful.

“Further consolidation in the market for this important kitchen staple will have real-word consequences for millions of Americans,” Jonathan Kanter, who leads DOJ’s Antitrust Division, said in a statement. Sen. Elizabeth Warren, Democrat of Massachusetts, wrote on Twitter that the ruling was a “bizarre outcome” and called on the Justice Department to “continue taking on anticompetitive mergers that would drive up the price of food.”

The episode exposes the headwinds the Biden administration faces in its effort to strengthen America’s antitrust enforcement regime. Conservatives argue that the administration is trying to undo decades of pro-business rulings with a new approach to oversight. Antitrust advocates inside and outside the administration say they are up against a hostile judiciary and a phenomenon that government scholars call “regulatory capture,” when regulators act in the interests of the entities they are supposed to be overseeing.

U.S. Sugar hailed Noreika’s ruling, releasing a statement last week that said the merger would allow the company “to increase our sugar production … and benefit our employees as well as customers throughout the country.”

The ruling wasn’t the only hit to the Biden administration’s antitrust agenda this month. A Washington, D.C. federal judge ruled last week that UnitedHealth could move forward with its $7.8 billion acquisition of Change Healthcare.

“They’re 0-2,” Douglas Holtz-Eakin, president of American Action Forum, a conservative think tank, tells TIME. “There’s no evidence that people who are reviewing the cases carefully are buying this new approach.”

The idea that consolidation leads to efficiencies and thereby lower prices is deeply entrenched in the minds of jurists and regulators throughout the federal government. But in recent years, the political pendulum has shifted, with more scholars and politicians arguing that decades of relaxed antitrust enforcement has, in fact, led to higher prices, growing inequality, worse labor conditions, and too much political power in the hands of a small corporate elite.

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On the campaign trail and since he first took office, Biden has repeatedly highlighted the historic levels of economic concentration as troubling, and vowed to be the first president in four decades to reverse this trend.

He appointed anti-monopoly researchers to lead the two antitrust enforcement agencies, with Lina Khan as chair of the Federal Trade Commission and Kanter at the helm of the DOJ’s Antitrust Division. And he signed a sweeping executive order in the summer of 2021 directing the entire government to work toward cracking down on consolidated power and increasing competition.

The order put a large onus on the Secretary of Agriculture, Tom Vilsack, to rein in consolidated agribusiness, in large part by updating the rules of a 1921 law to protect farmers and consumers from anti-competitive forms of exploitation.

“It is very concerning that USDA would undermine DOJ’s antitrust efforts, which clearly contradicts the ‘whole-of-government’ approach in President Biden’s executive order on competition,” a senior congressional aide for a leading member of Congress focused on antitrust issues tells TIME. “Any merger that results in two giant players dominating a market is obviously bad for competition, and consumers will likely suffer through higher prices.”

The Department of Justice filed its lawsuit in November 2021 to block U.S. Sugar from acquiring one of its rivals. The merger between the corporations would “eliminate aggressive competition in the supply of refined sugar that leads to lower prices, better quality, and more reliable service,” Kanter said in a statement when the suit was filed. “This deal substantially lessens competition at a time when global supply chain challenges already threaten steady access to important commodities and goods.”

While the lawsuit already faced an uphill battle in the courts, where many federal judges have a long record of allowing such mergers to go through, members of the administration were caught off guard last spring when one of their own came to the defense of the deal.

Fresco, a 30-year veteran in the USDA, made a strong impression on the judge, according to the ruling, which was unsealed on Wednesday.

“There is no one at USDA with a longer tenure working on the Federal Sugar Program,” Judge Noreika wrote. “Dr. Fesco testified credibly that she anticipates the Proposed Transaction is not likely to lead to higher prices but, in fact, may lower prices for U.S. purchasers and consumers of refined sugar by creating certain efficiencies and cost savings.”

Critics of the deal were particularly struck by Fesco’s assertion that her analysis was based on her familiarity with the individuals at the sugar firms.

“We have a problem when we have civil servants who are actively flouting the democratically elected leader of the government that they work for,” Matt Stoller, director of research at the American Economic Liberties Project, an anti-monopoly think tank, tells TIME. “It’s outrageous what she did.”