David and exactly how much emotion and free will he really has. Fan opinions seems to range from him being entirely emotionless and simply following Weyland's orders to being entirely sentient and deliberately seeking out loopholes in his programming. Sound familiar?
Did he infect Holloway because Holloway was the most convenient target, or because he was the human who had been the biggest jerk to David? Also, since Word of God confirmed David had something of a crush on Elizabeth, there is a third potential motivation.
Fan Discontinuity: A very considerable portion of the fanbase has come to see both Prometheus and Covenant as just below Alien 3 as films they do not want to acknowledge as part of the Alien franchise, in large part due to the fact that the Xenomorphs origin as a bioweapon is recent, or that it ignores the fan favorite acceptance that at least some Xenomorphs are natural species living on different worlds.
Fan-Disliked Explanation: Many fans did not like this answer to the question raised by the Space Jockey. One of the main points was the reveal that they look like humans and not the elephantine alien beasts thought until then, despite the fact Ridley Scott had stated endlessly since that it was their suit which gave them that shape.
Fanon: People tend to believe Fifield is supposed to be Irish, as his actor is English and he generally looks an awful lot like Sheamus. However, nothing about his background has been officially released.
David mentioning that Ellie's father was killed by Ebola back when the film was originally released in 2012 may have made it seem like a distant, exotic disease to most people around the world. Then in 2014 an Ebola outbreak flares up again in West Africa, infecting several US caregivers and doctors in the region, killing one man who had visited relatives there and didn't get treated in time, and infecting one of the nurses who was looking after said man that died of the disease. Suddenly Ebola doesn't seem so remote any longer for those in the West that normally only saw news statistics about deaths in Africa from this disease.
In a less significant but still worth noting thing to mention, a lot of David's friendly interactions with Shaw becomes this considering that he kills her in Alien: Covenant.
The crewmen who have a running bet with each other throughout the movie, Ravel and Chance. While they are more likely just friends or at least on familiar terms with one another, the duo did have an awful lot of significant glances and nearly all of their screen time was with the other.
Also Millburn toward Fifield. He seems to be laughing at his comment early in the film in a way to gain his approval.
While the movie is a visually and aesthetically amazing piece, the plot and behavior of the crew is a mess. Just look at the Idiot Ball section to get an idea. Honest Trailers described the crew like this:
It's the Same, Now It Sucks!: A major weakness of Prometheus is how similiar it is to Alien. In particular, Alien was revolutionary for having its protagonists be Space Truckers, but here, when the characters are well-financed and highly motivated elite scientists, they still act like unprofessional dabblers and look like they have never been in a field research (or even a field trip, for the inconvenience).
Vickers' death became popularized by CinemaSins, who claimed Vickers graduated from "The Prometheus School of Running Away From Things". Though, this creates a case of Critical Research Failure, as in that scene, you can clearly see that there is falling rubble blocking her way, therefore she can only in a straight line.
Misblamed: Zig-Zagged. Damon Lindelof bears the brunt of the hate for this film by people who didn't like it, as now it's known that he turned the script from what was originally known as Aliens: Engineers into the first draft of Prometheus, so the blaming does have a basis. However, his treatment didn't end up being the final product either: he cautioned Ridley Scott against leaving so many mysteries unexplained, precisely because of the bad reaction to the finale of Lost, but Scott promptly overruled him and worked on Lindelof's ideas on his own way. There is ample evidence major parts of the film were rewritten, reedited, or reshot by Scott well into production; the much derided decision by the science team to remove their helmets, for instance, was not in Lindelof's original script.
One-Scene Wonder: A proto-xenomorph shows up only for the last minute of the film, and was a huge hit with the fanbase.
Paranoia Fuel: David can access the memories of the crew whilst they are in stasis. They've been in stasis for over two years. Furthermore entrusting your life to an amoral synthetic for that length of time is unnerving.
Signature Scene: Shaw's infamous improvised c-section to remove the monstrosity she's pregnant with.
Special Effects Failure: In a film that is by and large astonishing to look at, Guy Pearce's terrible aged make-up really stands out, the result of prepping a design on the fly during a then-tighter schedule. One could explain it in-universe as side-effects of Weyland trying to extend his age, but it can still be jarring or even creepy.
This film can be viewed as modernized adaptation of H. P. Lovecraft's At the Mountains of Madness. This is due to the fact that much of its first-act material was taken directly from Dan O'Bannon's original Alien script, which was essentially a rework of that story (the version we're familiar with was a root-and-branch rewrite by David Giler and Walter Hill). O'Bannon (like his friend and onetime collaborator, John Carpenter) was a major Lovecraft nut and would eventually direct The Resurrected, an adaptation of Lovecraft's The Case of Charles Dexter Ward.
Squick: A completely uncensored emergency c-section, anyone?
They Changed It, Now It Sucks!: When the original script for the film, Alien: Engineers, became available online and was confirmed as authentic, series fans were outraged over how superior it was to the rewrite, which removed all of the overt connections to the original film and introduced a lot of plot holes in the progress. Also counted towards as They Wasted a Perfectly Good Plot.
Heavily invoked by the "Happy Birthday, David" viral clip. David is shown making several odd gestures, including what appears to be a slight moment of processing when the narrator asks what he can do (tilting his head slightly with a glossy look in his eyes), and his speech about how war and poverty make him sad, complete with thorough waterworks, then (without missing a beat or changing expression) describing how he does not feel even the remotest emotion but can replicate them perfectly. He also "smiles" (note Sarcasm Mode) whilst claiming he can perfectly replicate emotion and fit in with humans.
Brought up when Holloway asks David why he's wearing an environment suit when he doesn't need to breathe. David responds by saying that he was designed to be as human as possible to put humans at ease when dealing with him. Not wearing the suit would put him squarely into Uncanny Valley territory.
The Engineers, first seen in the movie's intro. They look almost human, but are over ten feet tall, and even if the DNA is mostly the same, they genuinely seem to have about as much in common with us as we have with David.
WTH, Casting Agency?: It seems odd to cast Noomi Rapace as an English scientist considering she uses her own Swedish voice. The real 'WTH' moment comes with casting an obviously English child actress to play the young Elizabeth. The character being English isn't necessarily vital to the plot, so it would have been less jarring to just have Elizabeth be Swedish like her actress.
Vocal Minority: While certainly not perfect, this movie scored a respectable 73% ("Certified Fresh") critical rating on Rotten Tomatoes—far higher than Alien³, Alien: Resurrection or either of the two Alien vs. Predator movies—and its audience rating was almost as high. Still, to hear some longtime Alien fans talk about it, you'd think this film was a complete disgrace to the franchise with no redeeming qualities whatsoever.
Visual Effects of Awesome: Save for Guy Pearce's faulty makeup (which, as mentioned, can be explained in-universe), even those with a negative opinion on the film can agree that it looks incredible, especially in 3D. Some examples include but not limited to would be the opening shots of the waterfall and the world, The Engineer's sacrifice, and the Starmap.