Yes, the movie has so many What an Idiot! moments that this became the first movie ever to have an entire page by itself. Spoilers unmarked.
- Tennesse and Ankor go EVA to repair the damaged solar sails.
You'd expect: Tennessee and Ankor to operate on the buddy system, like anyone else in any other high-risk situation ever, keeping each other in view at all times.
Instead: Ankor heads inside as soon as the repairs are complete, leaving Tennessee to make his way across the huge solar sail array and back to the ship all alone.
The result: Nothing really bad happens, except Tennessee picking up the signal that lets the rest of the plot happen. Still, given the havoc the signal plays with both suit and the man himself, the Covenant could have lost Tennessee second, instead of him being one of two survivors.
- Newly appointed Captain Oram has just discovered a mysterious signal coming from an uncharted planet that has similar conditions to Earth but somehow was missed.
You'd expect: That Oram takes the sensible choice and leads the crew to their intended destination instead of going to an uncharted planet. While the conditions may appear suitable to life, nobody knows anything about potential biohazards, predators or other factors that would prevent the colonization.
Instead: Oram orders the crew to follow the mysterious signal.
The result: It kicks off the entire plot and condemns the lives of at least 2,000 people, if not entire civilizations.
- Okay, the atmosphere of the planet is breathable. That doesn't mean it's free of poison, parasites or any other possible hazard as anyone with half a brain would know.
You'd expect: That the crew bring protective suits and don't expose themselves to any unknown pathogen by breathing or touching it until they are completely sure there is not anything dangerous on the planet. Or alternatively, send their android first to run tests and determine if the atmosphere is really safe to breathe.
Instead: Not only do they not use helmets, they don't even bother to protect their skin. There isn't even any justifying dialogue, such as saying they have sampled the atmosphere and detected no harmful elements. They only had the make up of the atmosphere to go on, which only confirmed it was breathable.
Even worse: Sergeant Hallett goes around touching plants and breathing alien spores.
The result: Neomorph spores infect crewmen at will and they die via embryo through the mouth minutes later, giving birth to two dangerous predators who go to butcher more crewmen.
- Karine has been locked in the med-bay with a convulsing Ledwards who appears to have something tearing its way out of his back.
You'd expect: Karine to grab a weapon of some kind and get as far away from him as possible.
Instead: Karine walks up to him and hugs him.
Even worse: She can see something is bursting out of his spine, yet she places her hand right on the spot while hugging him.
The result: Karine is first wounded and then mauled to death.
- Ledwards is infected by alien spores, and while Karine was assisting him he threw up blood over her. Faris gets splattered by blood from the Neomorph bursting from Ledward's back.
You'd expect: For Faris to keep calm and composed, grab a weapon and lock the three people (including herself) exposed to the blood under quarantine.
Instead: Faris panics like a 5-year-old that has just seen blood for the first time in her life and locks Karine up with the dying Ledward and the beast that's bursting from his back (visibly disregarding the fact that she as been in direct, unprotected contact with them and might be infected as well, in true Zombie Infectee fashion). She comes back with a weapon, but it's too late for Karine who's mauled by the Neomorph.
Even worse: She trips over the blood, breaks her ankle, keeps falling throughout the way to the bay and misses every shot that she makes against the Neomorph with a freaking-shotgun in a hangar full of freaking exposed blasting-explosives.
The result: They blow up the ship in a routine worthy of The Benny Hill Show.
- Hallett's illness gets progressively worse and he eventually starts convulsing and vomits up an embryo.
You'd expect: The others to first of all, get away from him whilst he's spewing blood as it may be contagious, and when the embryo starts moving for them shoot the damn thing while it's disorientated.
Instead: They stand around looking at the monster for so long that it gets up and runs off.
The result: The Neomorph returns a short while later and kill two of them.
- Crew member Rosenthal was hurt by the Neomorph that burst out from Hallett's mouth, and in the ensuing chaos the creature disappeared. She knows first-hand how strong and fast the creature is (it ripped a crew member's jaw clean off with a tail swipe, for fuck's sake!).
You'd expect: That she stays with the main group. After all, refreshing yourself is not worth endangering your life with a dangerous beast in the loose. Alternatively she convinces somebody to help her clean up: you have somebody to watch your back, plus After Action Patchup beats Self-Surgery any day.
Instead: Rosenthal separates from the main group.
Even worse: She wandered off far enough that her agony screams couldn't be heard by anyone else. Despite Oram specifically telling her not to go too far.
The result: Rosenthal ends up killed by the Neomorph.
- Captain Oram has just killed the Neomorph that David was trying to bond with. He already knows the android is up to no good and doesn't have any reason to trust him.
You'd expect: Having dealt with the immediate threat, he puts David out of commission. After all, he's an android and they can bring his head aboard if they have any questions.note
You'd also expect: Oram to go back to his crewmates and tell them about everything he just witnessed.
Instead: He follows David to his creepy experiment stash and watches all of his horrifying specimens but still doesn't bother to incapacitate David, even when it's clear that the android is out of his mind.
Even worse: He follows him to a dark cavern filled with facehugger eggs, and for some reason trusts David enough to touch one of them.
The result: It opens and the rest is obvious, as pictured above.
- As Lope and Daniels flee from the Xenomorph they get to see David and Walter locked in combat.
You'd expect: Knowing that Walter is vital to them for being able to travel while in hypersleep and is a valued crew member in his own right, the two of them would kill David with the guns they are both holding and trained to use. They are presumably aware of Walter's Healing Factor, so they should know that even if they hit Walter by accident, he can heal from wounds, while David cannot.
Instead: They run away not even making a token effort to help and leave the android to fend for himself.
Even worse: Neither Lope or Daniels tries to wait for Walter in favor of fleeing for their lives the second Tennessee arrives. Maybe David has a point about how humans treat androids.
The result: Without help or witnesses, Walter is defeated and supplanted by David.
- The last that Daniels and Lope saw of Walter, he was locked in combat with David, who looks exactly like him. Then Walter turns up.
You'd expect: Them to make sure he is really Walter and not David wearing his clothes. All they have to do is cut him and see how long it takes to heal, or if it heals at all.
Instead: They let him on board the lander, without doing anything to make sure it's really him.
Even worse: The very fact 'Walter' still had unhealed cuts when he arrived at the dropship would have been concerning, because the real Walter's healing factor is near immediate. At least Daniels should have realized the ruse when 'Walter' was stapling his cuts despite having a healing factor.
The result: Surprise, it's David!
- After Daniels and Lope run away, David and Walter are left to fight without any witnesses. David manages to disable his opponent and decides to supplant him to aboard the Covenant. In order to adopt his appearance, he severs his own arm to simulate Walter's Neomorph bite and puts Walter's clothes on.
You'd expect: Him to run to the spaceship. As no one saw them fight, he only needs to replicate the damage they had watched Walter receive before their own eyes, which amounts to the lost arm.
Instead: Aside from cutting off his arm, David decides to give himself the exact same wounds that Walter sustained during the fight. This goes against the facts that a) the fight had no witnesses and thus nobody can assert the synthetic's identity by looking at his battle damage, and more importantly b) Walter can heal from these small knife wounds and David knows it, so the real Walter would have returned pretty much unhurt.
The result: Nothing happens, because as dumb as this decision might be, the crew is dumber, and they never realize this point.
- Daniels, Lope and Walter/David are saved by Tennessee, return to the Covenant and reunite with Upworth and Ricks.
You'd expect: As the rest of the crew have died from the Neomorphs and may have been exposed to the spores, the crew would quarantine themselves and discuss their next course of action together as well as performing medical tests on themselves in case of infection.
Instead: None of the crew are medically examined in case of infection leading to the Xenomorph bursting from Lope and running havoc on the ship.
Even worse: Upworth and Ricks, despite just finding out the rest of the crew members have been brutally killed while on the planet, decide to immediately separate themselves from the main group and have sex in the shower.
The result: A Xenomorph bursts out from Lope, runs havoc on the ship and brutally kills Upworth and Ricks.
Worse still: Had our showering lovebirds not played rock-music so stupidly loud during their literally steamy-hot sex, they would have heard the shipwide warning broadcast that a homicidal alien is now on-board, got dressed and armed, and maybe even survived the ordeal to have finished the round and enjoyed an after sex cigarette.
- David, still disguised as Walter, is putting Daniels into hypersleep. She asks him if he'll help her build her cabin on the new planet, as she and Walter discussed earlier.
You'd expect: David, being highly intelligent and skilled at deception, would say, "Yes, of course I will," and then put Daniels to sleep with her none the wiser.
Instead: David makes a face clearly expressing that he has no idea what Daniels is talking about, immediately cluing her in to his real identity.
The result: David puts Daniels into hypersleep anyway, because unlike everyone else in the film, his stupidity never comes back to bite him.