Dummied Out - There's a handful of lines of dialogue in the game's files that do not appear in the final game. At least one of these is obviously the first take of a line that did make it in, the original having even more awkward wording.
There's an entire folder of sounds labeled "Faggioli" that mostly consist of a voice distorted by radio static saying things to you and making quips while there is gunfire in the background. A couple of these remain in the game while you are fighting with Paolo, despite the fact that they are clearly neither Paolo nor anyone else who ever actually appears in the game.
Fake American - Arnold's ethnicity is not mentioned, but his voice actor is using an American accent instead of his native accent.
Talking to Himself - All of the main characters have unique voice actors, but just about everything else is voiced by one of the existing actors, such as the computer, or Doctor Morrison clearly being Arnold.
Orphaned Reference - There are strange lines of dialogue during the fights alongside Paolo that do not match any of the characters present. In the game files, these are listed under "Faggioli," a character who may have been an earlier version of Paolo, but does not appear in the game with that name or voice.
When you first meet Paolo, he tells you that you can yell at the hubbardium nutters to make them run, because they're apparently cowards. Arnold replies that he's seen it... except every enemy you've come across so far has been bloodthirsty and eager to use their gun, leading to what comes across as a misleading bit of Gameplay and Story Segregation.
After you witness Paolo's death, Arnold will make a comment to Bruce about not getting there in time and only seeing a recording. In the final game, you're in an air duct above the scene of the crime when you get the cutscene, with no monitors or cameras around. Furthermore, if you pay attention, you can see that there is no body through the vent below you, until after the cutscene. In other words, it's pretty clear that you're seeing it in real time in the final game, implying that the line with Bruce was from some earlier story draft in which you were intended to find out about the death in a different way.
What Could Have Been - Several different places, including the official website, report story synopses that range from slightly different to majorly different from the final plot. These include the implication that your job is to rescue the miners stranded on the asteroid (instead of just Warren and the rest being insane), or an entire plot about the mining being illegal operations setup to refine hubbardium into drugs for money, instead of simply being the Company's routine operation (which went bad when they Dug Too Deep).
Several places, including the box art and other promotional materials, show lots of different models and character designs that do not appear in the final game, some of which are clearly earlier designs for the final characters.