I think people are raising too many questions that doesn't matter really.I felt like i got the most important questions about the engineers answered.They created human life by sacrificing an engineer by drinking that black stuff in the cup,same black goo that was in that Room with the statue mixed with the planets resources(I think),like water was mixed with the goo the engineer drank.
What happened in that ship is not important,we know hell broke loose because of their experiments.
If there are something to be bothered about,it would be the poor character development,Fassbender stole the show while the rest was left in the shadow.Didn't care for any of them really.
I really wanted to think that this was the same planet as the one in Alien,it sure looked to end in a way that could make you believe that.The crashed ship,Engineer in his seat as seen in the original Alien,the Alien we are familiar with born.
The exit is one of the biggest WTF moments i have ever seen in a serious movie,a Woman taking an Alien ship and seeking revenge on the Engineers,ALONE

If it was for the escape,alright but going on another adventure alone taking on the engineers?
Like i said,i liked the story about the engineers and their purpose,but anything else the movie offered was nothing special.