The movie isn't perfect, but none ever is. I really don't have much of a problem with how this unfolded.
Did some of the characters do stupid things? Yes, most certainly. And I find that quite believable because in the real whorl people who should know better frequently do stupid things. These characters were not Starfleet starship personnel. They were all distinct individuals with most of them there to make a buck. Not much idealism in most of them.
Although it's not discussed or referenced the film unspokenly establishes the method of star travel in this universe. If they can reach another star system with a few years (specifically two years in this instance) then they have to have some form of FTL capability. On the flip side it's obviously not Trek or Star Wars type FTL because they also use some form of suspended animation for the crew. It makes sense because any trip lasting more than a few weeks or months is going to need a lot of supplies if the crew are awake.
I know it was just a cgi alien, but the death of the Engineer by the oversized face-hugger near the end was really disturbing. It really reinforces how truly nasty and deeply terrifying these xenomorphs are. They are truly frightening weapons. It isn't enough that they can kill so wantonly, but that they can kill in such an invasive way.