engineers ?

Maybe Shaw goes to the home planet, gets in a time machine and sets the black goo mutations on them. Partially joking but it would be a neat twist

We can't really say. The ship was not thoroughly explored and the only evidence we have are the holes in their suits and the head with some mutation. Presumably a bio-weapon was out of control and started infecting the Engineers or something went wrong with the Black Liquid and did something to some crew members and everyone that was awake went into panic run-for-your-lives mode. This basic instinct of survival portrayed by the engineers would mean they are alive and not robots also.