Nearly two weeks after two Supreme Court justices delivered a stinging rebuke warning lower-court judges not to “defy” their rulings, the judge at whom the directive was aimed issued an apology from the bench, pledging to adjust to meet the highest court’s demands.

The acknowledgment on Tuesday by Judge William G. Young in Federal District Court in Massachusetts highlighted the precarious position that lower courts have landed in this year as they struggle to make sense of a growing number of unsigned orders the Supreme Court has produced through the court’s emergency docket.

Judge Young’s apology came at a hearing on Tuesday to discuss how to move forward after the Supreme Court in August overruled his decision to block the Trump administration from slashing hundreds of millions of dollars in grants awarded by the National Institutes of Health.

Writing as part of that emergency order, Justices Neil M. Gorsuch and Brett M. Kavanaugh had suggested that Judge Young subverted the court’s will by failing to apply an earlier emergency order focused on canceled Education Department grants to his N.I.H. case.

Judge Young said on Tuesday that he had not realized he was expected to rely on a slim three-page order issued with minimal legal reasoning in April to his case dealing with a different agency.

“Before we do anything, I really feel it’s incumbent upon me to — on the record here — to apologize to Justices Gorsuch and Kavanaugh if they think that anything this court has done has been done in defiance of a precedential action of the Supreme Court of the United States,” said Judge Young, who was appointed to the bench by President Ronald Reagan in 1985.