"Within the Justice Department, officials have long chafed at some of the prisoner exchanges pushed by the State Department..."

"... in part because law enforcement officials tend to believe that authorities should adhere to a 'like for like' rule, in which only individuals of equal status or criminal history should be exchanged. For example, exchanging spies for spies has long been an accepted practice at both the State Department and the Justice Department — but federal law enforcement officials frequently object to proposed swaps of convicted criminals for people who committed relatively minor offenses.... Robert Zachariasiewicz, a former DEA agent who was involved in the case against Bout, said... 'We just showed that it is really useful to have an American in your back pocket because you never know when you need them to trade'....

From "In freeing Griner, Biden faced resistance abroad and at home/The president faced opposition from the Justice Department, which viewed a one-for-one swap involving WNBA star Brittney Griner and the notorious arms dealer Viktor Bout as a mistake" (WaPo).

Senior current and former Justice Department officials who work on such prisoner exchanges note that part of their long-standing arguments to foreign governments when they seek arrest and extradition of foreign nationals is that the United States does not pursue criminal cases for political reasons — but turning around and later swapping Bout or others after they have been tried and convicted sends a signal that politics does influence U.S. prosecution decisions, potentially making it harder to accomplish future arrests and extraditions. "Most people in law enforcement believe that America needs to be seen as a rule-of-law nation, and that we run the risk of undermining our own arguments around the world if we play that same game and politicize our criminal investigations," [said Bill McMurray, a former FBI agent]....

As for Paul Whelan, the "U.S. Marine veteran who is serving a 16-year sentence on espionage charges that the U.S. considers bogus":

For months, State Department officials had advocated a swap involving Bout that would include the release of both Whelan and Griner, but Moscow refused unless the United States also secured the release of Vadim Krasikov, a former colonel from Russia’s internal spy agency, said officials familiar with the matter. Krasikov is serving a life sentence for murder in Germany, and Berlin had made clear that releasing him was a non-starter, a U.S. official said....

“Sadly, for totally illegitimate reasons, Russia is treating Paul’s case differently than Brittney’s,” Biden told reporters at the White House on Thursday. Russia’s demand for Krasnikov, and insistence that it would only trade Griner for Bout, one-for-one, continued until mid-November....

“This was not a choice of which American to bring home. The choice was one or none,” [Blinken] said...