I've been wondering about something odd in the structure of the Military Commissions Act: it defines "unlawful enemy combatant" and "alien" separately in § 948a but then says military commissions have jurisdiction only over alien unlawful military combatants in § 948c.
I'm beginning to think the key might be Hamdi v. Rumsfeld. During the invasion of Afghanistan, the U.S. government detained Yaser Esam Hamdi. After learning he was a U.S. citizen, it transferred him from Guantanamo to a brig in Virginia, where it held him without bringing charges. In Hamdi v. Rumsfeld, the Supreme Court held that "a citizen-detainee seeking to challenge his classification as an enemy combatant must receive notice of the factual basis for his classification, and a fair opportunity to rebut the Government's factual assertions before a neutral decisionmaker." (More or less. It's a fractured decision, and two members of the plurality are no longer on the Court, so you have to count some noses.)
I haven't gone trolling through the Congressional Record for it, but perhaps Congress intends the "Combatant Status Review Tribunal or another competent tribunal established under the authority of the President or the Secretary of Defense" from § 948a(1)(ii) to be the "neutral decsionmaker" the Court requires for U.S. citizens.