Nobody, at any time, acts remotely like a scientist.
Goo DNA Scene = Is this really the best means available for this incredibly advanced species to introduce genetic material to a planet? It’s a little like finding out that Prometheus brought fire to humanity by setting himself on fire despite the ready availability of kindling. As with many, many other bizarre moments in this movie, this makes sense at a thematic and allegorical level, but fails at the level of elementary plot logic.
Weyland = Since Weyland’s plan involves him being revived once they’ve made contact with the aliens, he must know that this will be exposed as a deception within a day or two, making the whole elaborate ruse completely pointless, except as a setup for a lame third-act reveal. Weyland’s primary motive, we eventually learn, is the hope of learning from the aliens some means of further prolonging his life, as he has hit the limits of artificial extension and is near death. Except he can apparently remain alive in cryostasis indefinitely. So instead of funding a probe and further medical research while he waits on ice for the next breakthrough, he has packed himself on this unprecedented and incredibly hazardous voyage.
Crew = Upon arriving at their destination, we see that the team has incredibly sophisticated mapping probes, but charge into an alien facility themselves without waiting for the probes to finish scanning the structure. Immediately upon discovering that there’s a breathable atmosphere within the facility, one Dr. Holloway brazenly pulls off his helmet—chiding his colleague and lover to not “be a skeptic,” because apparently skepticism is anathema to good scientists. Though it’s later confirmed they have no way of being sure the air isn’t full of strange pathogens, and everyone else points out that this is insane, the rest of the team nevertheless immediately follows suit when it doesn’t result in his instant death.
Fifield and Hoodie = The Shaggy and Scooby of the film—a biologist and a geologist—freak out at the sight of dead alien bodies, despite having been willing to truck 35 light years on a perilous exploratory mission, and hasten to head back to the ship in a panic. They get lost, despite the fact that the geologist is the one with mapping expertise. This fear then evaporates as quickly as it appeared, as the biologist decides he should recklessly cozy up to a terrifying alien serpent creature. To nobody’s surprise, it quickly kills the biologist, while his geologist colleague is dissolved in black goop, only to later reappear as a zombie in a completely pointless fight scene. This is a pattern. In almost every scene, members of this handpicked group of top scientists for a trillion-dollar mission routinely make the kind of wildly irrational blunders that we strain to accept when it’s half-drunk teenagers in slasher pics.
David and Holloway - Android David infects one of the scientists with the black alien slime for no apparent reason, despite the obvious danger this poses. The aforementioned infected scientist can see there’s something obviously wrong with him, but instead of immediately seeking medical attention, decides to risk himself and the entire crew—including the love of his life—by pretending he’s just hunky dory until he literally collapses.
Squid Baby - Because… how the hell does he (David) know what “three months” looks like? When she pleads with him to cut it out, he attempts to knock her out and put her in stasis, again for reasons unclear. She then neglects to mention this unsporting behavior to anyone, and nobody seems at all curious when she shows up bloodied and bedraggled after performing an emergency auto-caesarian. David, who was previously so keen to retrieve squid-fetus for whatever reason, exhibits no interest in what might have happened to it.
Space Jockey Pilot - A member of this incredibly advanced species that created humanity is found in stasis and awakened. Confronted by a group of humans, including an android that speaks its language, and obviously lacking any knowledge of how many others there might be, or what weaponry they might have, this advanced being makes no effort to gather any information. It roars and begins acting like a space monster, attacking the party with its bare hands. The Engineer survives this crash and almost instantly locates Noomi Rapace in order to continue the effort to kill her, again with his bare hands.
(Prometheus) is less like deliberate mystery and more like simple bad writing.