In the NA version of Prime 1, some Space Pirate logs talk about the Metroid Prime, discussing the armor they made for it, its morphology, etc. However, the Metroid Prime lives in the Impact Crater, and the Space Pirates never make their way to the Impact Crater itself, thanks to the Chozo Artifacts. So how do they even ''know'' about the Metroid Prime?
* They supposedly found it wandering around in a tunnel while they were drilling. This opens up the rather large plot hole of why didn't they just keep on drilling if the crater barrier isn't as impassible as previously thought, which is probably why it was changed in the European and Trilogy versions...but then ''that'' opens the plot hole of why does Prime have obviously artificial weapons (missile launchers etc.) on its first form if none of the technologically-advanced races made contact with it?
** The first form ''you'' see isn't the first form ''they'' saw. Wasn't there a log that said it assimilated their weapons? And since they were developing Beam Troopers at some point, and the pirates with packs have missiles...
** The problem is that that log was changed in the EU version and Trilogy, which means that canonically, no, the Pirates never directly encountered it and thus it couldn't steal their weapons. That's why this particular JBM discussion is even taking place.
** Could just be that a few Pirates got lucky and stumbled across it, but were killed and had their weapons stolen. That would explain why they never logged about finding it: they never survived the encounter.
* The easiest explanation to the North American is that the pirates found it but it escaped. Then the Chozo sealed it away under the temple that contained the bulk of Phazon.
** Nah, the Pirate Logs show that the Chozo were long gone by the time the Space Pirates arrived, with the Temple and Artifacts already identified as blocking the Impact Crater prior to the encounter with Metroid Prime.
** Except the Chozo came back briefly to seal away phazon and their own logs detail the pirate's failures. The Chozo just left because they couldn't handle being around phazon too long. Further the pirates do talk about encounters with ghosts, they don't realize those "ghosts" are the returning Chozo.
** It makes a lot more sense that the pirates' weapons were involved in Metroid Prime's armor, since they match, but since you find identical discarded armor on Phaaze, it's clear that's no longer canon. Instead that's just a natural part of the Metroid Prime life cycle.
*** The Space Pirates didn't create Metroid Prime's carapace in any version. Even in the original NA version, it was specifically a phazon mutation.
** However, it has just occurred to me that A) phazon can affect machines as well as animals and B) phazon turns out to be one huge spanning conciousness. Maybe it just copied the pirates' weapons remotely and started adding it to each new phazon metroid. It'd explain those fission metroids that have weaknesses to specific samus-beams.
*** Or it just grabbed some Chozo weapons when it fought them. That also has the advantage of explaining why it's beam weapons have the special effects when the Space Pirates were never able to copy those.
* Here's my theory on the issue. We don't know what the leviathan's journey was like. For all we know, it plowed through a space pirate ship somewhere along the line, and some weaponry was embedded into the leviathan, as well as a Metroid. Upon landing on Tallon IV, the PAL/Trilogy version of events happened.
* This whole situation is actually a result of ContinuityDrift. Keep in mind, when Metroid Prime was being developed, the only games we had in the series were Metroid, Metroid II, and Super Metroid. The origins of the metroids themselves were still a mystery. Metroid Fusion would reveal that the Chozo created the metroids on SR388 to serve as a predator for the X, but that game wasn't out yet (indeed, it came out on the same day this game did), so the metroids were much more of a mystery. Keep in mind that the NA Gamecube version of Metroid Prime was an early/unfinished version (they kept working on the game for 8 more months, resulting in a FAR more complete/polished version for EU). In the NA release, Metroid Prime really was a phazon-mutated metroid. After the reveal of the origin of metroids in Fusion (and the "how did it get into the impact crater when it was sealed" plot hole), Retro decided to go a different direction with the story, resulting in EU lore becoming canon (as that version was the basis for the Wii Trilogy version in the US). This ended up causing Metroid Prime to become an ArtifactTitle. In the future, the title would be used for all 3D games in the series, while the 2D games kept the original Metroid title. We actually never found out what the "Metroid Prime" creature was in the updated's never explained.

Why did the Pirates build doors too small for themselves? I'm not even talking elite or Phazon variants either. Luring a bog standard Space Pirate to a door reveals that they're about a foot taller than the doors of their facilities.
* In the space ship/crash site, you can see MASSIVE doors. Those are probably 100% space pirate. As for the others, they either scavenged them from chozo stuff, and simply duck through the doorways.

Of all the things that Samus learned about Phazon from her experiences, one would think it might be pertinent to figure out what happened to the Gravity Suit when it was dunked in Phazon, turning it into the Phazon Suit. It has no negative effects on the wearer (at least as long as they're inside the suit) and in fact makes their resilience higher as well as protects them from the effects of blue Phazon. This seems like it might have been useful to try and replicate later once it was known that Phazon is a galaxy-wide problem.
* Except we do know what happened. The suit was infected by the vertigo strand retro virus, which infuses phazon into a subject in a less deadly, less violent madness inducing manner. That's how the Elite Pirates and Omega Pirate were created in the first place. Now Samus does have some knowledge of biology but at no point in the games is she seen with the resources necessary to duplicate that.