---A ship with 2000 colonists, out in the middle of nowhere, years away from home/help... only has one shuttle? Really? REALLY? The Colonial Marines brought a spare dropship, and go figure, it came in handy. Redundancy is super important when you're years away from help.
---You're going to risk your one and only shuttle flying through a severe hurricane? Okay... couldn't you have just, like... waited for it to pass? It's established later that you didn't know how long storms last on this planet. For all you knew, that storm was going to pass in an hour or two, but hey, let's throw our shuttle right on into that shit, everything'll be fine!
---What's the deal with the ship's captain always joining the away team? This seems like a SUPER bad idea, yet this trope is everywhere.
---No environment suits? Really? I mean, sure... the air is breathable and whatnot... but what about bacteria and allergens? You brought along a biologist to poke around at stuff, and she had no objections to this? Are you sure she actually earned her degree/doctorate? I mean, I've seen people put on full HAZMAT suits to clean hotel rooms, nevermind land on alien planets that nothing is known about. The average janitor takes more safety precautions than these people.
---The AR-15 platform is apparently still being used for new rifles, 80+ years in the future. Not outside the realm of possibility... just kinda boring.
---Did nobody ever go over containment procedures with any of the Covenant's crew? I mean, I can't really fault Covenant specifically, since Dallas and Lambert were pretty quick to break quarantine too. Maybe it's a company-wide problem with Weyland/Yutani.
---Way to go, Tennessee! Risk the structural integrity of the Covenant, putting the lives of all the colonists at risk, to maybe save a couple of the away team? Real officer material, right there! Par for the course for Weyland/Yutani, apparently.
---Whose genius idea was it to put the husband of the shuttle's pilot in a position of authority with a responsibility to protect the colonists? Conflict of interests, much?
---There are scary monsters out there killing everyone... LET'S SPLIT UP, GANG!
---Do any of these red shirts even have names? IMDB says they do... but I honestly couldn't attach a name to a face outside of the main characters while I was watching the damn movie.
---Monsters take dozens of hits from assault rifles and shotguns, not slowing down at all. Fine. Maybe those guns just don't fire particularly powerful rounds. The Pulse Rifles seemed to have no problem, but then, those were firing explosive-tipped light armor piercing rounds. Maybe the Covenant was stocked with airsoft rifles.
---Monster is killed by just a few hits from one of the Covenant's airsoft rifles, because it's plot-important, and the shooter is one of the named hero characters.
---Named hero character immediately has his hero character status revoked in the dumbest possible way. A suspicious-behaving robot freaks out and starts acting all shady - then asks the acting captain to shove his head inside a giant fleshy pod - on a planet already established to have all sorts of deadly biological weapons and monsters (which are ACTIVELY KILLING HIS TEAM) - and the response ISN'T riddling the robot with airsoft pellets? No wonder the acting captain risks everyone's well-being on checking out this planet, the dude has no sense of self-preservation.
---More advanced robot, with apparently different structural weaknesses (which are shown to be unknown to the less advanced robot), is somehow defeated by the less advanced robot. Alrighty. Possible, but dumb. I guess David scored a lucky critical hit.
---Robot switcheroo! Who didn't see this "plot twist" coming? The hair cutting scene pretty much SCREAMED that this was going to happen sooner or later.
---Boy, that alien sure did get big fast. I mean, the franchise has always been a little iffy on the timetables when it came to the Xenomorph lifespan... but geez! That thing went from being the size of a little yappy dog to full-grown in, what? 20 minutes?
---Creature is killed by... THE CLAW!
---Daniels isn't showered with pressurized acid? At that distance? 'Kay...
---David cuts off his own hand to mimic Walter. Makes sense, and is easy enough to accomplish with that big knife he had. But how did he manage to conceal the hole in his chin from the nail necklace that Daniels stabbed him with? If David didn't conceal it, how did Daniels NOT notice it while patching up his face? If Daniels is suspicious of the robot, which she CLEARLY is initially, why did she completely ignore this wound? Did David pull a Face/Off and switch faces with Walter so he wouldn't have the chin wound? If yes, how did Daniels not notice THAT? Clearly these robots don't instantly heal physical damage.
---Not really a problem with the movie, but I want to see the conversation Daniels would have needed to have with the colonists whose trucks and building supplies she blew out the airlock. "Yeeeeah.... soooo, we went off-course without consulting anyone, based on a whim from acting-captain Dumbshit - oh, did I mention that my husband, the actual captain, was cooked alive in his stasis pod that the company assured you was perfectly safe? Anywho... we found this random planet that no one noticed before 'cause they were having a kickass concert, and Tennesse is like, a HUGE John Denver fan, so we had to stop. Denver was already playing, so we skipped the environment suits to get there faster. Long story short... the shuttle is gone, everyone who went down there is dead, we traded our robot for an older model with better musical taste, and let a monster on the ship that stole a pair of our trucks. And that, Mr. and Mrs. Jones, is why we can no longer build your home."