A military court judge delayed the sentencing phase in order to review the motion to dismiss the case.
The judge said Bergdahl faces up to life in prison.
Obama's successor, Donald Trump, heaped criticism on Bergdahl during the 2016 presidential campaign.
Bergdahl has said that he left his post and meant to alert people about problems he perceived within his unit.
"I can't comment on Bowe Bergdahl because he's - as you know, they're - I guess he's doing something today, as we know", Trump said October 16. He entered a "naked plea", meaning he does not have an agreement about the sentencing terms with prosecutors.
Former Army lawyer Eric Carpenter said the judge has to worry not only about whether Trump has directly influenced the case, but also what the public thinks under a military justice concept called apparent unlawful command influence.
Trump has been a vocal critic of Bergdahl and the Obama administration's decision to exchange five prisoners in Guantanamo Bay for his release in May 2014.
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President Trump has inadvertently thrown a wrench into the final stage of Army sergeant Bowe Bergdahl's trial.
The Army soldier who was held captive in Afghanistan after leaving his station pleaded guilty last week to desertion and misbehavior before the enemy.
"The member of the public that we are interested in maintaining confidence in the military justice system ... is going to be influenced by context", Nance said.
Nance seemed unsatisfied with that explanation, calling Oshana's interpretation "strained".
Bergdahl elected to be tried by a judge, not a panel of military officers, in August.
The judge, who said there was no doubt he could be fair and impartial, did not immediately rule.
Bergdahl told investigators he snuck away from his outpost in 2009 with plans to run about 20 miles to Forward Operating Base Sharana in order to bring attention to what he saw as serious issues and leadership mistakes within his unit.
Many others, including members of his own platoon, say Bergdahl's disappearance placed other soldiers in Afghanistan at risk as the Army scrambled to find him.