The Rolling Stone article tries to act like Bowe snapped under stress, which is not at all what he's saying in Serial. He'd only been in Afghanistan for 3 months, and the Serial podcast said that he hadn't seen any real action yet (Rolling Stone talks about combat he was in).
The vast majority of his complaints are par for the course in the Army -- mass punishment and the constant feeling like the higher command is stringing you along. It's, like, what the Army's all about. As you gain in rank and your perspective widens, you end up being the person who makes some PFC spend 5 days guarding an MRAP, and you just shift your hatred to the next level up the chain. Bitching about the higher headquarters that is just one level above your visibility is what people do in the Army.