- The ship has landed in the planet and they are exploring the Engineer structure in their spacesuits. Holloway detects with his scanner that carbon dioxide levels are low enough for the air inside to be breathable.
You'd expect: The crew to wait to perform analysis in order to rule out the possibility of microorganisms, pathogens or any kind of hazard the air could be carrying before even considering working without their suits. Still, even although it were deemed to be safe, they should keep their suits hermetic anyways in order not to bring with them any terrestrial biological residue that could deteriorate and/or modify the environment. Most of the crewmembers are either scientists who will know the importance of asepsis in an exobiological research or space pilots who should be familiarized with the consequence of not following containment protocols.
Instead: Deciding that not choking in the atmosphere is fair enough for him, Holloway takes off his helmet.
Even worse: While other crewmembers do object to it, nobody tries to stop him. Instead, they imitate him once they see the air is really breathable.
The result: Nothing this time, but in an alien planet with unknown lifeforms it could have caused literally anything. The next film, Alien: Covenant, would show it in a very graphic way.
- Two members of the expedition team (Fifield, a geologist, and Milburn, a biologist) set to leave the alien facility and return to the Prometheus. The first of them is the mapmaking expert of the crew and the controller of two floating cartographic drones that are presumably still mapping through the tunnels.
You'd expect: Them to reach their destination safely. If they get lost, all they have to do is check Fifield’s wrist computer for the three-dimensional map of the corridors he just created.
Instead: They get lost, but neither of the two thinks of doing such a thing.
The result: The next point.
- Fifield and Milburn come upon a pile of corpses who all have exit wounds in their heads. They radio in to the ship's captain, justifiably freaked out, and tell them their position. Janek tells them he's been getting a glitch from one of Fifield's mapping probes that is situated at the end of a long corridor.
You'd expect: That, since Janek can see the stranded team members' location on his comm system and can direct them, he would tell them to wait near the entrance of the structure until morning. Or, failing that, he would tell them to stay exactly where they are and not touch anything - literally, anything besides the course of action he takes.
Instead: Janek laughs at their discovery, acts like the glitched probe isn't a problem, and leaves them to wander around some more in the structure. A few minutes later, he goes off to have sex with Vickers and leaves the comm station unmanned.
The result: Milburn and Fifield are left to their own devices, leading to the next point.
- Milburn and Fifield are camping in the "big head" room, where they discover that all of the jars on the floor are leaking black liquid. A snake-like creature emerges from a pool of the liquid and Milburn wants to examine it. Fifield tells him this is not a good idea and that they should leave immediately.
You'd expect: Them to leave immediately and don't look back. After all, both of these men were smart when they bugged out during Shaw's discovery of the first Engineer body in this very room. Milburn is also a biologist, so he should completely know the risks of approaching an unknown creature. Even if he is really that fascinated with the damn thing, it's much safer to retreat for now and maybe return later with a support team and adequate tools to capture and analyze the creature. Heck, even someone without an extensive education in biology would probably notice the creature's striking similarity to the terrestrial cobra and give it a wide breadth.
Instead: Milburn continues goading the creature, and even begins stroking it.
The result: The creature latches onto Milburn's arm and breaks it, which leads to Fifield falling into a pool of the liquid and having his helmet melt into his face.
- Captain Janek receives Fifield's signal in front of their cargo door. He tells the crew the open it to check him, and they all see what seems to be Fifield's corpse bent over in a bizarre posture.
You'd expect: The crewmen to approach it cautiously and weapons in hand. They have just witnessed Holloway getting horribly mutated and have every reason to think Fifield might have suffered the same fate.
Instead: They stroll towards it casually and unarmed, and one of the crewmen even goes to kick it.
Even worse: Janek clearly senses something is wrong with the body, yet only mumbles to himself instead of yelling at his crewmen to stop and take caution.
The result: The thing gets up, revealing itself to be certainly a mutated Fifield, and promptly wreaks havoc, killing at least three men.
- Shaw realizes that she had sex with her boyfriend after he'd been infected with a biological agent that heavily mutated and killed him. She's pregnant—despite being sterile—and a surgical suite extracts a freakin' octopus monster from her womb.
You'd expect: Shaw to alert the ship's medical team that she should be placed in quarantine to see if she's infected, or- at the very least- tell somebody that there's a mutated octopus monster in the captain's cabin.
Instead: She doesn't breathe a single word to anybody about anything that happened, and the octopus baby is completely forgotten about until it becomes Chekov's Gunman and kills the rampaging Engineer at the very end of the film.
The result: Actually nothing, but it's only by sheer luck no other crew were killed by the thing.
- Mr. Weyland orders David to wake up the sleeping Engineer in order to convey his wish for more life.
You'd expect: That he understands they are dealing with a creature whose motivations, abilities and power (or even sanity, as it's likely the last thing the Engineer saw before going to hypersleep was the dramatic demise of his race) are completely unknown, and as such, that they have to act with extreme caution in their interactions with him.
Instead: As soon as the Engineer is awake and looking at them, Weyland orders David to issue not a request, but a demand, without any kind of introduction or preparation whatsoever. (In a deleted scene, the Engineer gets understandably angry at this, yet Weyland still addresses him a way that even by human standards would be incredibly rude and overbearing.)
Even worse: Weyland orders one of his bodyguards to hit Shaw while in front of the Engineer, thus offering him a free show of how petty and violent humans have become.
The result: If the Engineer wasn't already convinced he had to destroy mankind and reinitiate life on Earth, he probably became so by this point, and if he was, it didn't help a bit. He kills Weyland and his crew and activates his spaceship to carry on his plan.
- Shaw and Vickers are seeing how the fallen Engineer spaceship has landed on its round edge and is tumbling towards them. They run away before it crushes them.
You'd expect: That they look around in order to try to pinpoint where is the spaceship going to finally stop in order to avoid the place. Their helmets allow enough peripheral vision to get a good view over their shoulders and it will not take much extra time.
Instead: They run in a straight line from their initial positions without ever considering the possibility they might be running to their deaths.
Even worse: They actually look back to the spaceship, yet still keep running straight, clearly trying to outrun it lineally. They don't even consider simply getting out of its way.
The result: The spaceship catches up with them, crushes Vickers, and almost crushes Shaw, who trips over and only then comes up with the above solution.
- With everybody dead except for a decapitated and treacherous android, Shaw is stranded on the planet. Said android knows how to pilot an Engineer spaceship, which is done basically by playing a flute and pushing buttons. However, he asks her to reassemble his body and trust him for the rest of the journey.
You'd expect: Shaw not to trust David. He previously killed her lover For Science! and absolutely nothing will stop him from doing the same to her if she lets him. In their situation, she should keep David's head disembodied, take it to a spaceship and demand him to program it automatically for the journey, the last while explaining to her what he is doing in every step in order to prevent a trap. This is admittedly not devoid of risks, but it is still the safest plan.
Instead: She trusts David fully and repairs him.
The result: Alien: Covenant.
What An Idiot / Prometheus