Most of what the NCIS investigates is penny-ante crap on bases. They blew their first high-profile case out of Iraq (the Lt. Pantano case). There may have been political pressure, but the simplest explanation is that the NCIS was in over their heads and just couldn't handle the investigation. So they cut corners and here we are.
Honestly, I have not followed the case that closely so it is difficult for me to pass judgment. It just seems to me there must be some 'outside' influence required to get people to eat their own for no reason.