Everything depends on the person, as different people are open to different conversations. If they're open to conversation and seem like a rational person, have them help you understand their decision. There's a very good chance it makes perfect sense, if explained from their eyes. If they're the "because they're a piece of shit" type who might not be open to explaining themselves rationally, it's best to not present the question at all and I'll explain why.
Assuming they're of higher rank than you, there's a lot of ego and pride involved. Even if questioned proffessonally, they take a hit to that pride and some store that like a baby elephant, never to forget that one time you questioned them. It's not the right way to lead but you have probably already seen this everywhere. They'll wonder if the punished airman is talking behind their back or if they put you up to it. It'll be a hit to their pride. A way around it may be to ask, for future reference when you're they're rank how and why to handle the situation. This takes the personal touch out of it and makes it more hypothetical. There's a lot of people in leadership positions but few leaders. My advice when questioning poor leadership is to:
Read the type of person you'll get and predict their willingness to entertain your questioning.
Decide which hills you're willing to die on. I took a lot of hits I probably shouldn't have, knowing that in the long run, it would benefit me more to not challenge a minor decision if doing so would make the situation worse for everybody.