I always felt that there was an element of stupidity throughout the series. More so out of sheer panic and the fact that these characters, despite their qualifications, are in over their heads.
- Kain approaching the eggs, and Dallas bringing back Kain back to the shit. Disregarding quarantine.
- Gorman disarming the marines and sending them into the hive on their rescue mission. Also, Burk trying to sabotage the mission in order to bring back samples to the company.
- The prisoners generally fucking up and 85 giving in to WY's orders to land on Fury 161.
- Prometheus, which mostly goes without saying.
In this one, I felt like there wasn't too much out of the ordinary. Tennessee's order to lower ship initially bugged me, as he was risking the entire colony, but it ended up working to get a signal through regardless. For me, complaining too much about how stupid the characters are in this series sorta goes against one of the main motivators for the plot of all of them.
It's about how believable in context the action is. Alien and Aliens both take great care to establish why decisions that seem dumb are made: in terms but f the character and the context.
From Alien 3 onwards this has been increasingly skipped as the films struggle to differentiate while offering up the expected scares and creature action.
Take Alien.
They actually bicker about investigating at all and it's made clear they have to according to their contract.
Kane is established as the eager one always searching ahead and a bit too nosy for his own good: of course he - nervously - takes a peek in the egg.
Dallas is established as weary Captain of a beat up tug and Kane as a friend as well as second in command: of course he chooses to break quarantine and not sit in the airlock with a strange creature while Kane dies particularly with panicky Lambert backing him up. Ripley sticking to rules actually helps this make sense and makes clear Dallas is already out of his depth handling this kind of emergency.
Brett goes looking for the cat because Parker told him to. Brett is Parkers right hand guy and will clearly do whatever he asks. He's embarrassed he messed up and the creatures only a small snake at this point. He doesn't look too happy about it but of course he can't lose further face with Parker and he dutifully follows orders.
And so on. Every action in Alien makes sense in context for the characters and even plays into how events unfold. For example of course Ripley survives she's been the most competent and adaptive from the beginning.
Covenant (and Promethous before it) are simply not as well crafted in this regard. Little to no justification is provided and characters feel mostly like cyphers doing what the plot demands. They're sub par next to Alien by a wide margin in this area (others too but I'd digress).
Cameron also did a good job in Aliens making decisions believable in context and as with Alien often used Ripley, Hicks or Vasquez (Bishop too) to counterpoint the others losing their cool and making questionable decisions or suggesting questionable ideas.