What I believe a lot of people miss about this brilliant movie is the fact that there are not any real heroes or villains. Everybody is just doing their job to the best of their ability.
Lt. Kafee is pursuing his job at determining the truth & pursuing justice. Col Jessup is pursuing his job of operating a military base, which sometimes involves doing things outside of "text book procedures."
The only failure (& it is a significant one) on the part of any of the characters is that when Jessup is shown to have been responsible for the failure in his "non standard" practices, he needed to take responsibility for that failure rather than try to make others pay for the consequences of his choices.
I'm an air traffic controller, I have a lot of rules that were largely crafted by lawyers to reduce the liability of the FAA. There are plenty of circumstances where following those rules to the letter would actually produce greater risk to a flight than to break the rule. That is because aviation has far too many variables for any rule maker to create a "perfect" set of rules that can cover every possibility. Know the rule that you are breaking & if it goes badly, you have to take responsibility for your choices.