That's the thing, they aren't random. They're just filled with symbolism. Once you understand what they mean then it starts to make sense. You should also check some of the cut scenes. There's this dialog between the engineer and the humans that explains why he attacked them.
Maybe his mistake was to go way too deep with symbolism, it really isn't what people expected. They wanted a simple easy to understand sci fi blockbuster and they got anything but. If this was from an indie foreign director people (by people I mean people into foreign/artsy flicks) would praise the shit out of it. But it's the mainstream guy from Alien and Gladiator...
.
No man, I don't mean "symbolism". I mean scenes like a random zombie appearing before the ship, people opening the entrance for no reason, fighting the zombie and then nobody ever mentions that thing again. I mean things like David "poisoning" the husband for a reason that is never explained or even implied. I mean things like Wayland faking his death for no reason at all. And of course the famous "running away from falling space ship in a straight line" or "let's try to pet an obviously dangerous alien cobra because reasons".
Maybe there are cut scenes that explain stuff like this but if there are, they should have put them in the movie or cut the scenes that make no sense without them.
I mean the script was written by Damon Lindelof who is famous for making shit up and never trying to explain it because "it's symbolism man, drink it innnnnn" (he written Lost).
Here's a good vid:
Some of these thing are obviously nitpicking but most of them explain why watching this movie can be painful.
And don't get me wrong I still liked it but I remember my initial feeling of disappointment after watching it. Could have been great, but is just ok.