The Danza: One of the mercenaries, Vladimir, was portrayed by Vladimir Furdik.
Deleted Scene: Prior to the film's release, Scott said that 20 minutes of deleted scenes would be included on the home video release of the film. Several moments seen in the trailers are not present in the film - most notably, the mutated Fifield attack scene was intended to be much longer and set at a different point in the film (happening just as Weyland, Ford and the mercenaries head out for the structure).
Executive Meddling: A fairly egregious example: it was the studio who hired Damon Lindelof to 'edit' Jon Spaihts' original script; if you watch the making-of doc The Furious Gods it becomes clear that this muddled too-many-cooks factor is what led to a lot of the confusing and unclear plot elements. Spaihts flat-out says that he wasn't thrilled with the decision to hire Lindelof, but understands that the studios wanted a well-known name in the credits.
Supposedly, however, the (hoped-for) resulting franchise is going to go its own way in regards to plot, presumably focusing more on the Engineers. This turns it into some ungodly hybrid of prequel, Spin-Off series from Alien and Backdoor PilotforAlien.
Another Flip-Flop occurs in regards to the Engineers/Space Jockeys. In Alien, the signal picked up by the crew of the Nostromo is revealed to be a warning to stay away, and some of the characters muse that the race must have been extremely noble to make their last act such a warning (not just for their own kind, but any species). In Prometheus, the Engineers/Space Jockeys are revealed to be nowhere near that noble, and according to Word of God now, actually are all monstrous assholes. Then again, it HAS been nearly 35 years since Alien, long enough for Ridley Scott to change his mind/get more cynical.
The final narration suggests it was Shaw, not the Engineers, who sent the message.
Lying Creator: Ridley Scott seemingly made some real effort to misdirect people about the film, likely to create some degree of surprise when it was actually released.
He constantly moved back and forth over whether the film was a prequel to Alien to the point it was finally "confirmed" as being loosely set in the same universe. The actual film is definitively a prequel and firmly part of the Alien canon with several notable nods to the film. Then again looking at all the promotional features and trailers all but confirms it anyway.
He also claimed that Vickers was the Final Girl from the outset. During the film, there are some hints the character could be this after all. However, it turns out to be a Red Herring, as only Shaw and David survive.
Lastly he claimed that there would be no xenomorphs. However, a form of xenomorph makes a brief appearance in the last scene.
Method Acting / Enforced Method Acting: All over the place. As seen in the making-of documentary The Furious Gods, Scott repeatedly told the crew not to tell the actors certain things or to let them see storyboards to procure more genuine responses, notably in the scene where a snake-like creature bursts from the dead Millburn's mouth; the actors were unaware that that was going to happen, and Kate Dickie's shriek of surprise is quite real. Theron also noted that she was very nervous about (repeatedly) setting the stunt man on fire for the scene in which Vickers kills Holloway, thus giving the character a believably conflicted attitude. (Her mild Heroic BSOD over it is expanded upon in a deleted scene with Janek.) And mutant!Fifield was originally going to be an entirely-CGI creation, but they eventually decided to let actor Sean Harris do the scene himself with extensive prosthetic makeup. Harris was perfectly willing to be set on fire for the sequence, prompting even Scott to call him a "crazy bastard."
Name's the Same: Charlie Holloway has almost exactly the same name as Charles Halloway, one of the main characters in Something Wicked This Way Comes by Ray Bradbury. This one is served with a bit of cruel irony, though: the movie was released in the United States just three days after Bradbury's death.
Elizabeth Shaw also shares her name with the first companion of the Third Doctor on Doctor Who.
Viral Marketing: Includes a futuristic TED conference with Peter Weyland, the unveiling of the new "David 8" model and an "official website" linking to Weyland Industries, detailing the timeline of the company and its accomplishments. When the end credits finish rolling, there is a Weyland Industries logo and a date; 10.11.12.
What Could Have Been: Original drafts of the script would have included more elements from the Alien franchise; including Holloway dying via chestburster, and different motives for Weyland. Jon Spaihts' original draft was more closely tied to the original series and set the movie up as a direct prequel to Alien while still leaving room for a sequel featuring David and Shaw (or Jocelyn Watts, as she was originally known) going to the Engineer's home world, and averted most of the Idiot Ball moments introduced in the rewrite. The main cause of this seems to be David Lindelof's (the writer for LOST) attachment to the film.