Prosecutors Say It's Unclear Papers Chaplain Carried Were Classified. You can never be sure about a legal case you read about in the papers. There's so much texture and detail that gets lost in even the best newspaper report. That said, the case against Capt. Yee is giving off a certain stench of shambolic military CYA.
Would a white Christian chaplain get smeared with accusations of being a spy, get threatened with the death penalty, get locked up in solitary for three months, all over documents that the government isn't even sure are classified? As for the adultery charge, note that it's an offense only if it interfered with discipline—and apparently the affair was neither in the chain of command nor at all public. And by getting that testimony in first, then recessing the trial, the government manages a second round of strafe-and-smear.
Based on the news coverage, it sure looks like some combination of three things is going on: (1) Major government vindictiveness against someone who was effectively ministering to the Gitmo detainees and/or major government anti-Muslim bigotry [plus shades of Wen Ho Lee?]; (2) All that, plus the government is now throwing up whatever charges it can to cover up the fact that it smeared an officer without reason; (3) the prosecutors really think he's guilty but cannot prove it and/or are totally incompetent.
The information that is public makes the 'really guilty' story seem much the least likely alternative.