The alien, presumably killing supposedly started life on Earth. Exactly how does adding your DNA eventually evolve right back to match humans? There are some other theories that might make more sense scientifically. But why leave it so unclear?
If it is not Earth, how can the engineer breath? They were terraforming the planet for a reason I suspect. Which brings me to a minor point ...
How did he go from his crashed ship to the escape pod.
The tattooed geologist was a huge asshole. If you're hiring people to work together in the darkness of space, you might want to hire someone who works well with others.
The main character, when prompted for evidence on why she believed the engineers built us, simply said "It's what I choose to believe". No legitimate scientist would ever use the faith argument as an argument.
Assuming the black goo started humanity, I have no idea what it actually does. If you:
- ingest a lot - you immediately die, but you go on to spawn life on another planet
- ingest a little - you slowly turn very grey sick
- have sex with someone who has ingested a little - get pregnant with a "GIANT" face hugger
- get it and acid sprayed in your face - turn into a zombie monster
So, right before the Engineers were going to kill everyone on earth, an out-break happened, preventing them from killing us. How fortunate.
You're an alien that's been asleep for two thousand years. You wake up, immediately kill people who were not being threatening and try to complete that mission. Perhaps things have changed?
You've discovered a powerful Alien race very intent on killing humanity. Should you take their war ship back to them, reminding them that humans are still kicking, just to ask them some questions? If you are going to say hello, at least use the WMD on them.
Why is it so easy to get access and activate these WMDs? They would be far more deadly than a nuke but you just have to screw off the top and ... monster!
You're a industrialist bent on extending your life. When asked if you want to ask the alien questions, you reply "I don't care".
Why is a ladder necessary to reach the controls. Yes, I understand the aliens are all 7-8 feet tall. But, we still put access controls at slightly above mid-height.