More recently, a conservative website attacked her nomination to the Treasury Department, accusing her of being part of the “deep state” and blaming her for a “sweetheart plea deal” with James Wolfe, the former Senate aide who pleaded guilty to lying to the F.B.I. about his contacts with reporters.

Ms. Liu’s office struck an agreement in which Mr. Wolfe pleaded guilty to one charge of making a false statement; two other charges of the same offense were dropped. Prosecutors recommended that he be sentenced to two years in prison, but a judge sentenced him to two months, in line with the sentencing guidelines.

Fox News has amplified the critique of the Wolfe case, and Mr. Trump on Tuesday echoed it on Twitter. He did not address significant differences in the cases, including the fact that Mr. Stone did not admit his guilt and forced the government to go through a trial, that a jury convicted him of many more offenses, including witness intimidation, and that Ms. Liu’s office recommended a sentence of two years for Mr. Wolfe, not two months.

When it became clear that Ms. Liu would not stay until she was confirmed, it raised suspicions among some in the U.S. attorney’s office. Those were only compounded in late January when Mr. Barr designated Timothy Shea, a longtime trusted adviser, as her temporary successor rather than letting her top assistant serve as caretaker.

Mr. Shea arrived on Feb. 3 with David Metcalf, another perceived Barr loyalist, to serve essentially as his chief of staff. Mr. Metcalf immediately caused discord when he moved a prosecutor from her office so that he could work adjacent to Mr. Shea, according to two people familiar with the move. A Justice Department official said Wednesday that the office next to Mr. Shea’s had already been vacated.

One week later, they faced a dilemma when the four career prosecutors working on the Stone case proposed recommending a sentence of seven to nine years, in line with nonbinding federal sentencing guidelines.