The text of the bill is more confusing, mainly because it’s so long. However, I believe the offending part is Sec. 1032 (a), which states that the military “shall” hold a person captured in the course of the war on terror in military custody until the military can determine the person’s disposition under the law of war.
There does not appear to be a territorial limitation on this directive, so it probably also applies within the United States. Sec. 1032 (b)(1) specifically states that the requirement to take to detain a person in military custody doesn’t extend to U.S. citizens. So, it’s not required, but does that mean it’s still allowable? Is it now OK to detain an American citizen in the U.S. without the traditional protections of the Bill of Rights?