This is one of the roots of the problem. Once you have a class of people without rights, you can arbitrarily identify people as part of that class and they have no chance at due process. Unless absolutely everyone has basic legal protections, no one has them.
Edit: In other words, they were not recognized as a proper army and were deemed to be something like internal rebel forces, subject to internal law only, with no International protections, such as the Geneva Convention. They were treated horribly when taken into custody and often tortured.