More specifically in the situation, the officer who she needs permission from is an ex-lover and there is no real reason for her to listen to the guy. She's a bounty hunter, not a soldier under his command. It was just a reason to explain why Samus couldn't just use all the power ups she had from previous games from they very start, but they picked the stupidest and most misogynistic explanation for it. Also problematic in Other M is Samus spends way to much time expressing her feelings of inadequacy over not having a man in her life, when she's always been shown as a strongly independent woman. Basically they took one of the strongest feminist icons in gaming and did a 180 turn on her personality for that game.