It's not just that one scene, though. It's also that scene where Samus sees a Metroid and stares at it and then Adam shoots her and says "No! Don't shoot that Metroid, because shooting it with an ice beam might not work!" and then after she gets knocked out cold, her suit turns off (because her suit is powered by her emotions, which is a very practical system, because when she experiences any emotional shock, the entire system fails immediately (this is clearly what is depicted in every other game)), and she crumples defenseless to the floor, Adam shoots the Metroid with an ice beam and it works. And when she regains consciousness, he explains to her that these are special Metroids that are immune to the ice beam, even though that one wasn't I guess because it's a baby? but maybe probably all the other Metroids (which we haven't seen) can't be frozen, and that's why I had to shoot you Samus why do you do this look what you made me do Samus do you think I enjoy shooting you. Because the ice beam is now apparently absolutely the only possible way to kill a Metroid? And also because if that Metroid had turned out to actually even be one of the ones that the Ice Beam doesn't work on, then if Samus had tried shooting it, something bad might have happened? Even though she wasn't about to shoot it anyway, because she was so busy thinking about how she's a girl and stuff? I guess?
Or how when Samus is walking around in her suit during the game, she's like a foot taller than the other women in the game, but then at the end, when she's standing by a window and her love interest guy walks by, he's like two feet taller than her, because we can't have Samus being taller than her man now can we, so apparently Madeline Bergman is like one feet tall.
Or that plot twist about Madeline Bergman. They turned Mother Brain into an anime girl. There is no excuse for that.