whew, there are so many problems with this film it's hard to know where to start, but I'll pick just a few...
(Spoilers below, so if anyone hasn't see it yet, stop reading)
The implication that the "Engineers" genetic code infected ours, or even originated our is ludicrous.
Well, I certainly don't agree with this. Then entire point of the opening scene is that the 'Engineers' started ALL life on our planet. There's exactly zero evidence showing something like that didn't happen (indeed, the 'genetic material hitting the earth via comet' theory is a widely-accepted possibility).
The idea that a bunch of cave drawings could lead us to a distant planet and that "scientists" would read into the meaning of those drawings as an invitation to visit them is painfully simplistic.
Yup, that part was stupid. You wouldn't be able to identify the correct star system based on drawings like that.
A bunch of scientists going into a strange alien structure on a new planet and take their helmets off to test the air. Then they get lost. Then they argue. Then some of them become assholes and others that start out as wimps suddenly get brave when an alien snake shows up.
That part I'm okay with, as it's long been my experience that people do stupid and illogical things on a regular basis.
A lady has a squid baby by C Section and then recovers well enough to run around a few minutes later. A robot infects a crew member with black goo, which causes a "thing" come out of his eye, he then has sex and fathers the alien squid.
I think this is based on a misunderstanding of the plot and what the weapon being developed by the Engineers really was. The 'weapon' they developed was a rapidly evolving biological agent - tiny bits of DNA/whatever, that when exposed to the proper environment rapidly self-replicated and directed their evolution towards creating the weapon we know as the Alien. Once the weapon was in the dude's body, it rapidly took over - and apparently was transmitted to another's body via the impregnation process, something that makes sense given the later version of the Alien's method of reproduction: implanting a rapidly-growing object into the body of a living host. The crewmember who got infected wasn't the father of the 'alien squid' at all - which was just a mega-sized version of the Facehugger from Alien.
Re: the c-section thing, we all laughed about that a bit, but the robo-doc did stitch her back up and administered a shitload of pain meds, so it's at least possible that she could move around a bit.
To me, these are pretty small quibbles compared to the biggest two problems with the movie:
1, the timeline was - as many of these sci-fi movies tend to be - totally off. We won't see development of those technologies in 60 years from today. It would have been a lot more believable to have the movie set a hundred years after that.
2, there was never any discussion or explanation for the fact that Humanity apparently had control of artificial gravity by that point, a feat which would bring about such a revolution in human technology and advancement, in a wide variety of ways, as to make many of the plot points obsolete.