Why would the NCIS fabricate evidence? What does it gain them to see these soldiers convicted?
Career points. Convictions uber alles. It aint a successful investigation if there's no body in the lock up afterward.
Also, if you paid any attention during the previous decade, it was all the sudden "trendy" again for anti-establishment types to join such organizations to make sure those eeveel monsters in the US military didn't get away with anything.
There's also a tendency toward a bureaucratic mindset that demands that any investigation means guilt - period. And when guilt cant be established, that only means the guilty was too smart to get caught.
It serves a political purpose and helps make a clean name for those who prosecute.
It provides a clean name for those who accuse.
It helps coverup things that actually go on.