Character mistake: In the end credits of the Italian version, several roles are listed with blank spaces instead of the Italian voice talent. There are also inconsistencies with the same roles listed for the on-screen actors (for instance, two different words are used to translate "Homeless man" and "Clerk"). The Psx version also features spelling mistakes ("assestants").
Other mistake: For the "true" ending to happen, you toss the dagger to Scully; this happens while you are held at gunpoint, with the knife that has to fly right past the enemy, who does not react or show any surprise or awareness in the movie clip that follows.
Audio problem: The Italian localization uses a professional cast of voice actors, including for the main roles the official dubbers of the TV series. However, there are very small filler voice clips, such as the recorded voice mail and answering machine messages, that were recorded by uncredited performers who were not even native speakers.
Plot hole: Wilmore keeps busy (or straight shoots, really) the two agents outside Rauch's house. Meanwhile, Mulder leaves him to get to the secret facility. One wonders how, since they are in the middle of Alaska, he doesn't have a car, and there's no reason why he wouldn't help Wilmore killing the bad guys, so he can get his car, or the agents'.
Factual error: You decide to investigate the russian ship "Tarakan." The captain says "it's not far from here", and the characters take what looks like a leisurely stroll on the dock from their position. If you look at the in-game map, the two dots are on opposite sides of the bay.
Audio problem: You can take a snapshot any time with the in-world camera. It does not make much sense, considering that you can do that during videos that are shot in 3rd person instead of the standard 1st person perspective. In other words, you can take pictures of yourself that are not selfies and nobody could have taken them. If you can suspend your disbelief about it, there's still a glaring glitch; when you view the pics you took, the audio output at the time was saved too and plays again.
Other mistake: The suspect James Wong in international localizations of the game (Italian and Spanish that I could personally check) has two discordant dates of birth on the same official FBI file; one is 10/04/1948, the one and only in the English version, the second inside the body of the notes is 11/01/1950.