Haven't read the manga, I still didn't think it made any sense, especially factoring in all the other games.
I really could go on and on and on (and gladly will!) about Other M, but I DO think it deserves all the backlash it got and then some. To this day, I still have never seen a game just trample all over its heroine, one of the most progressive in the who gaming industry, and regress her - figuratively and literally - to such an incompetent, useless, and emotionally unstable wreck whose own greatest adversary wasn't Ridley or Space Pirates or Mother Brain but her own fragile, womanly emotions and unresolved daddy issues.
If anything, reading the manga made the scene even worse, because in the comic it's implied (more than implied, actually) that she manages to overcome those insecurities and fears, and she was still a child at that point, not a veteran survivor and experienced hero of countless adventures and wars.
But there's no CONTEXT for players. Showing that quick flashback made no sense to new players because the scene is not explained or elaborated upon. Even if you've played the games, this scene is never experienced in any of the games. ONLY a little-read Japanese-only manga gives the merest hint of what she's experiencing, and even THEN, as I stated above, Samus in that story comes to terms with it and has growth through accepting the experience.
You can't just plop a random scene without any context in the middle of a game designed "for new players" and then be confused when none of them know what's going on. For a game meant for newcomers, a great deal of it is reliant on obscure material and lore that the majority of players never once experienced or read or played.