Justice Amy Coney Barrett’s grilling of the solicitor general during oral arguments on nationwide injunctions on Thursday puts in sharp relief President Trump’s emerging problem at the Supreme Court — notwithstanding the conservative majority on the high bench.

That challenge was underscored by the high court’s halting, on Friday afternoon, of Mr. Trump’s efforts to use the 1798 Alien Enemies Act deport a group of Venezuelan migrants to El Salvador. By a seven to two vote — Justices Samuel Alito and Clarence Thomas dissented — the justices reckoned that the administration’s due process provisions “did not pass muster.” The case is now returned to the Fifth Circuit of the United States Court of Appeals for further proceedings.

Mr. Sauer, in the birthright citizenship case, was urging the justices to end the use of universal or nationwide injunctions by federal district court judges. The case came to the Nine via an emergency appeal from the government in litigation over whether Mr. Trump’s executive order banning birthright citizenship is crosswise with the Constitution. 

The Department of Justice, following a string of losses across three different cases, chose not to litigate the executive order on the merits. Instead, the government asked the Supreme Court to end the ability of a single federal judge to stymie Mr. Trump’s policy from coast to coast. Yet the solicitor general, D. John Sauer, was faced with skepticism not only from the court’s left flank, but also from its conservative jurists. That could spell trouble for the government. 

The DOJ could not have been happy when, during oral arguments, Justice Barrett and Justice Elena Kagan appeared to align in their concern that by opposing nationwide injunctions, the government was really seeking a warrant to evade judicial orders. Justice Kagan, a liberal lion, asked Mr. Sauer if he would commit to following a court order within the circuit it was issued. Mr. Sauer evaded that question — but it was picked up by Justice Barrett. 

The justice asked Mr. Sauer if she understood him “correctly to tell Justice Kagan that the government wanted to reserve its right to maybe not follow a Second Circuit precedent, say, in New York, because you might disagree with the opinion?” Mr. Sauer responded, “Our general practice is to respect those precedents, but there are circumstances when it is not a categorical practice.”

Justice Barrett, who was nominated to the bench by Mr. Trump, responded, “This administration’s practice or the long-standing practice of the federal government?” Mr. Sauer said, “As I understand it, long-standing policy of the Department of Justice.” To that, Justice Barrett asked, “Really?” The justice’s tone — arch and skeptical — suggested that she was doubtful with respect to that claim. 

A legal scholar, Joshua Blackman, argues that Mr. Sauer had the best of the argument, meaning that it has been the practice of executive agencies to “nonacquiesce” to an appellate court’s ruling with respect to persons who were not parties to the review tribunal’s judgment. Professor Blackman cites a memorandum issued by the Office of Legal Counsel in 2010 taking the position that the administration would no longer defend the Defense of Marriage Act. The solicitor general at the time was Justice Kagan.

Another conservative sage, Will Baude, in 2015 advised the Obama administration that if the Supreme Court ruled against it on ObamaCare, the administration could “announce that it is complying with the Supreme Court’s judgment — but only with respect to the four plaintiffs who brought the suit. This announcement would not defy a Supreme Court order, since the court has the formal power to order a remedy only for the four people actually before it.”

Justice Thomas appeared open to curtailing nationwide injunctions — he reckoned that “we survived until the 1960s without universal injunctions,” to which Mr. Sauer affirmed, “That’s exactly correct.” Justice Alito also appeared sympathetic to Mr. Sauer’s argument, reflecting that judges, whom he called “monarchs” in their courtrooms, are “vulnerable to an occupational disease” of overstepping their authority. 

Justice Barrett and Chief Justice Roberts, though, have tended to align as something of a swing vote within the court’s conservative bloc. In March, the two jurists sided with the court’s liberals in refusing the administration’s request to block a lower court judge’s order requiring the payment of some $2 billion in foreign aid.

More trouble for the administration at the high court could await in the case involving the deportation of an alleged member of MS-13, Kilmar Abrego Garcia. The justices ordered the administration to “facilitate” his return to America, but the Trump administration has so far resisted and asserted the state secrets privilege in the case. The presiding judge, Paula Xinis, heard arguments in that case on Friday. The high court’s ruling with respect to the Alien Enemies Act made a point of noting that the administration is “unable to provide for the return of an individual deported in error to a prison in El Salvador.”    

Oral arguments offered another warning sign for the administration, when Justice Neil Gorsuch reflected, “Well, Justice Kagan asked my questions better than I could have.” Justice Gorsuch wondered: “How do you suggest we reach this case on the merits expeditiously?” That suggests the case could come back to the court on the merits. If it does, it looks like Mr. Sauer will have further persuading to do if birthright citizenship is to end.