It should be noted that this is one of the few Resident Evil games to translate the original Japanese script subtitles into English. This makes it easy to tell what was changed in the voice acting script and what was originally meant to be said.
In "Research Report 220329", the Tyrant prototype "091" is instead referred to as the "T-091" in the localization. This is incorrect because the Tyrant is named after the version of the tG-Virus used to create it (ver.0.9.1) and is not a simple "batch number".
The introduction to the "Reconstructuring Notice" was cut in places, thereby removing the explanation for Morpheus D. Duvall's dismissal. It also erroneously implies that he was blamed for the Raccoon Incident, while in the Japanese version, it was actually alluding to the Arklay Mountains incident.
In the file "Ship's Log", the September 21 entry was noticeably cut-down. The fact that Umbrella had brought B.O.W.s onto the ship was replaced with a mention of the Captain fearing that "the ones" having escaped. It also removed the fact that the Captain was hearing strange noises, thereby begging the question in the localization as to how the Captain inferred that the B.O.W.s had escaped, despite the crew reporting nothing out of the ordinary. In the September 22 entry, the presence of an "armed gang" (Morpheus' men) occupying the ship is also missing.
The "Operator's Notebook" clarifies that a number of Umbrella workers at the wate disposal facility had been killed in an accident. In the Japanese version, the author also questions how long he will survive in the facility.
In the "Architect's Memo", the bio-sphere's designer is concerned as to how Morpheus will handle running the base since his dismissal. In the Japanese version, he refers to the Arklay Mountains incident in May that led to his dismissal as a "so-called 'biohazard'", though the English version alludes to Raccoon City, instead, which was destroyed over a month after his dismissal.
The second half of Research Report 220120 was removed in the translation, which clarified that there was a Queen (女王?) and Guard (衛兵?)-type.
In the cutscene where Bruce and Fong Ling meet, the latter reveals she knows his first name. In the localization, she reveals Bruce's surname, as well. Bruce adds in that Morpheus is 'blackmailing' both the US and China; this is completely absent in the Japanese script.