Yes, it's a plot hole which was fixed in later releases, but which created another plot hole.
First of all, your question is more than a little confusing, because it apparently quotes two logs from the first version of the game, the NTSC (North American) version, and two from the updated PAL version. (Notably, the NTSC version was released before the Japanese version, and the latter also changes the story in accordance with the PAL version.) So to support your question you quote two different, and contradictory, plots, which is fine because you're asking about this contradiction – but you don't quote the entirety of either of the plots, which is a little confusing.
The first and second logs you quote, log 11.156.9 "Impact Crater" and log 11.452.8 "The Key", are from the updated PAL version. The other two, log 11.156.9 "Metroid Prime" and log 11.377.1 "Prime Breach", are from the first NTSC version. (You also quote the two different versions of one of the logs, log 11.156.9.) Since you're asking about the plot hole in the NTSC version, here's the version of the second log you quote from that version:
We are particularly interested in a number of curious Chozo Artifacts we have been able to recover from a number of religious sites on Tallon IV. These relics resonate with power, and yet we are unable to harness them in any way. Science Team is attempting to fuse them together with Phazon, believing that a link might exist between them. We know that these Artifacts are linked to the Chozo Temple that block full access to the Impact Crater. We have yet to crack this enigma, however. Command grows impatient regarding this matter: results must be produced soon.
In addition, here's one NTSC log you don't quote at all:
Metroid Prime continues to feed and grow ever larger in the impact crater caves. Its hunger knows no bounds, and it has begun to manifest unusual mutations since its breach. These include armor plating on its epidermis and mechanical outgrowths that generate defense screens. These screens render it invulnerable to most weapon systems, but a flaw in the mutation leads to increased vulnerability to certain weapons. It compensates for this by shifting the screens quickly. This latest development concerns Security units greatly: they feel it's a matter of time before Metroid Prime corrects this defect and renders itself invulnerable to all weaponry. Containment would be nigh impossible if this were to occur.
As you surmise, there's a contradiction in the original NTSC (North American) version of the game. If we put together the logs from that version in chronological order by the log numbers – log 11.156.9 "Metroid Prime", log 11.377.1 "Prime Breach", log 11.402.5 "Prime Mutations" and log 11.452.8 "Chozo Artifacts" – the original story goes a little like this:
The Space Pirates, during their Phazon mining on Tallon IV, found Metroid Prime in a cavern, which is either the Impact Crater itself or adjoining caves that it had escaped into. It was a Metroid which was extremely adaptive to Phazon, and they watched it evolve rapidly, developing defensive armor plating. During one of its break-out attempts it adapted an ability called "assimilation" which allowed it to absorb and attach Space Pirate tech and armor to its body; technology it still possesses in both versions of the game when Samus fights it.
This assimilation is also the ability it uses when it steals the phazon suit from Samus and fuses with it in a last ditch effort to survive, thus becoming Dark Samus, which also happens in both versions.
In addition, the Space Pirates manage to find several of the Chozo Artifacts that unlock the Impact Crater, but they fail to discover their use.
The problems with this story:
As you found out, the issue here is that Metroid Prime is fought inside the Impact Crater. Nobody, including the Space Pirates, managed to enter the crater since the Chozo force field was erected, until Samus Aran unlocked it and entered herself.
Another issue is that in both versions of the game, Samus finds all the Chozo Artifacts in their original locations where they were hidden by the Chozo, and use them to unlock the impenetrable Impact Crater where she fights Metroid Prime. None of them are in the Space Pirates' possession.
The retconned story, and the issue it raises:
This was recognized as a plot hole by Retro Studios, who retconned it in the PAL version by removing all the references to Metroid Prime in the Space Pirates' logs. The new version of one of the logs you quoted as well as the one I quoted above are as follows:
Analysis continues on these accursed ruins and the Chozo temple that hovers near them. We are now completely certain that the containment field denying us access to the impact crater is linked to strange artifacts that belong in the temple... but we are no closer to finding them or deciphering the riddles that seem to cover every wall of this ruined place. Command grows increasingly anxious for a resolution to this matter, so we must redouble our efforts. X-ray squadrons will begin terrain sweeps within days - until they begin, patrols are instructed to report any and all architectural anomalies to their commanders.
We have come to another dead end. It is clear now that we will never discover the locations of the Chozo's artifacts until we can decipher the messages carved into the statues in this abominable temple. Our language databases are woefully inadequate, and our linguistic analysts can come up with little more than vague theories. The best hypothesis we can offer is that finding the artifacts will require items spiritually linked to the Chozo civilization. However, without these items, we are lost, and Command grows more impatient by the day. Results must be produced soon.
Putting these logs in chronological order as well, together with the PAL logs you quoted – log 11.156.9 "Impact Crater", log 11.402.5 "Gate System", log 11.402.5 "Artifact" and log 11.452.8 "The Key" – we see that the new story unfolds like this:
The Space Pirates find the Impact Crater, but are unable to breach it. They realize that mysterious Chozo Artifacts hold the key to unlocking it, but never find any of them. From power readings, they recognize a massive creature residing within
This retconned version of the story makes much more sense in-universe, solves both issues I mentioned above, and was also carried forward to the Nintendo Wii version of Metroid Prime, and is considered the canon story. So the answer to your question is that yes, this is a plot hole, which was retconned and fixed and is not really an issue anymore.
This retcon caused another contradiction, however, which the astute reader will already have recognized. When Samus reaches the inside of the crater and fights Metroid Prime, it's still in possession of Space Pirate technology. Where did that come from in this version of the story, where it never meets the Space Pirates?
There are a couple of possible explanations to this new plot hole later in the series.
It's obvious when you fight Metroid Prime in Metroid Prime that the initial intention was that Metroid Prime had assimilated Space Pirate technology, as chronicled in the NTSC version's logs. However, in Metroid Prime 3, Samus finds discarded pieces of armor that look like Metroid Prime's armor on Phaaze, the planet that is the source of Phazon. Perhaps its resemblance to Space Pirate technology is just coincidental, or perhaps the Space Pirates originally discovered this Phazon tech and "pirated" it on some other world. Or, perhaps not:
In Metroid Prime 3 it's also revealed that Phazon is more than just a highly radioactive mutagen: It's a giant, galaxy-spanning consciousness, and Phaaze itself is a sentient planet that seeds the galaxy with Phazon to expand its reach. Perhaps the Phazon encountered Space Pirates somewhere else than on Tallon IV and assimilated their technology, which made it available to all the different strains/seeds of Phazon on other worlds, including Tallon IV?
Since Samus finds what looks like a Metroid Prime husk on Phaaze, as mentioned, one implication could be that it's not a Metroid at all, but that it came from Phaaze. However, another log entry ("Leviathan Infant") from Metroid Prime 3 offers an alternative explanation for Metroid Prime's origins, namely that it started out as a regular Metroid on Tallon IV and was absorbed by the Phazon. I've cut out irrelevant (and spoilery) information, but the context here is that the "Leviathan" is the Phazon "seed" sent out from Phaaze, which impacted Tallon IV in the Impact Crater:
The Leviathan is capable of interstellar travel, creating wormholes in space to expedite the journey. Instinctively, it homes in on its planetary target. Shortly after impact, the bioform dies, leaving its armored shell to protect the Phazon core. Before it dies, the bioform often attracts and enthralls a large local predator. After mutating it through intense Phazon exposure, it compels the creature to protect the core. The core then begins to seep into the planet, replacing the local ecosystem with one based on Phazon.