The engineers are supposed to have engineered...us, right? That is shown at the beginning of the movie, with the self sacrifice, somehow seeding the initial life on Earth. Panspermia.
But if that was the case, that would have been 4.6 billion years ago. So why did life on earth develop plants and fungi? Why so many wildly varying species. Why didn't they all look humanoid from the get go. Why did it take 4.6 billion years, to go all the way through invertebrates, fish, amphibians, reptiles, mammals, apes to finally get to the ultimate goal of resembling the engineers. 4.6 billion years is stupendously long time for a species to remain the same, physically, technologically, culturally and ideologically.
Perhaps the idea is that many branches of science such as biology, paleontology, paleobotany, geology, etc, were thrown out by this new discovery, and life on earth is much much younger than the evidence suggests.
Alternatively, they came just a few million years ago and their DNA just mixed with apes, who already happen to look similar to engineers (and have compatible biochemistry) by a totally remarkable example of convergent evolution.
I am perfectly willing to suspend my disbelief for any scenario for the sake of fiction, but it has to be clear and consistent. I just don't get the main premise of the movie. Were they planning to come back to earth to kill all humans, or all life? I suppose it is to be explained in the sequel.
Now, I understand this is just fiction, and that evolutionary/biological plausibility is not a high priority, but I want to ask this very simple question: did they seed ALL life on earth (which is suggested by the prologue), or just human divergence from apes?
The answers here also suggest they created all earth life.