- First off, Samus's entire escapade with Adam's military unit is a problem in of itself. At the beginning of the manga's second volume, Samus and two other aliens are essentially a Federation Police Squad that typically do not meddle in the affairs of the military. After liberating a Space Pirate strong hold that triggers the snowball leading up to Zero Mission itself, Adam comes in and Samus and her squad really don't know who he is (or at the very least, do not react to him in any way shape or form). So the problem is, when in the world did the flashbacks of Samus w/ Adam's squad even take place? There's only one real place where that could have happened...
- And that brings me to my next point: Samus and her squad goes to Zebes (How she even got to Zebes is another problem, but I'll get to that in a moment) after Ridley and his forces take it over, capturing the Chozo that are left (and the Space Pirate grunts end up being brainwashed by Mother Brain). Suffice to say, this mission doesn't go over that well and Samus is forced to flee from Zebes. However, Samus liked the feel of going rogue and doing things on her own regardless. She explicitly states that this was the reason she left the Galactic Federation and became a bounty hunter and not over some dispute with Adam. Some years pass between this incident and the start of Zero Mission, which is the only place her military career could have started outside of the possibility of her joining the military first, the crap with Adam happens, and then somehow going down the police. That theory is a bit problematic when considering Samus doesn't react at all to Adam's presence when he shows up. Plus...
- Adam and Samus are actually on a fairly friendly level up to the events of Zero Mission regardless, not the rather terse level that Other M implies. Hell, at one point Samus raises the price of her bounty hunting services to a point where Adam finds it obscenely expensive and makes it a point to get the job done before the military came up. Hell, Adam even cracks a couple jokes with Samus (Other M goes far and beyond to show that Adam is SUPERSERIAL at all times). At this case, it's just out of character-ness.
- The Chozo who raised her and even Mother Brain explicitly state that Samus was notorious for being a lone wolf and disobeying orders from virtually everyone, something that they note has not changed when she was in the Federation to when she got out of it. This makes it pretty hard to swallow that Samus would be fine with Adam's authorization in Other M regardless.
- Speaking of Adam, I find these scenarios pretty odd. The first example is from the manga, the next two are from Other M.
Samus: I know that Zebes was attacked by the Space Pirate mothership with a black hole cannon, that there will be absolutely no back-up, that the Space Pirates already have Mother Brain and vastly more significant forces, and that this is essentially a suicide mission. But damnit, I'm going to try to help them any way, save the survivors, and beat the Space Pirates since I have the best chance of doing so. So me and my alien crew are going rogue with this police ship.
Adam: Okay, sure. You have two days to get this done.
Samus: Your brother is in this part of the ship and you're planning on detaching it? I have the most technologically superior power suit known in the galaxy and there's at least a good chance that I can get him back!
Adam: No. You might die and duty comes first.
Samus: There are unfreezable Metroids in Sector Zero. But when considering that I still have the best shot of taking out the Metroids with my plasma gun than you do with your Assault Rifle, I think I should probably go in and take care of this.
Adam: No. You might die, duty comes first, and I must sacrifice myself.
Seriously, kinda weird that Adam doesn't even deliberate on the first option despite how there was a significantly less chance of success than the other two and the first plan didn't even work in the first place.
- Samus goes through a traumatic event much worse than she did in Other M when seeing Ridley. She passed out and even went into a suicidal wreck after learning that Ridley probably ate the bodies of her parents. But... Samus kinda bounces back, goes into a rage, taunts Ridley during the fight, and even finishes with a hot-blood Conan the Barbarian-esque battle cry after he died. With all her talk about how she "was a different person from before," kinda weird that she kinda... lapses back in a rather odd moment in Other M.
- Some one on GameFAQs tried to bring up that the Prime series wasn't canon because Space Pirates (Zebesians) were only intelligent under the direct influence from some one like Mother Brain. This isn't really true when considering that before the Pirates even meet Mother Brain, a captured Space Pirate was pretty intelligent enough to try to sway Samus's alien teammates by recounting instances of Federation prejudice against their species. And then taunts Adam because he fell for an extremely obvious decoy meant to distract the Federation from Zebes. Plus, Pirates typically talk too.
- Not a plot hole/retcon exactly, but the manga stresses that the top-brass and leaders of the Galactic Federation are actually mostly aliens. In fact, the Chozo admit that they were in part responsible for the creation of the Federation in order to unite alien races. Kinda strange that all we've seen from the Galactic Federation in Other M, Fusion, and Prime 3 are humans.