The Movie: In the movie's enigmatic opening scene, an Engineer drinks the black goo, whatever it is, and dissolves into bare DNA, which then appears to make a new cell. This is apparently the first "seeding" of life on Earth (or at least, human life — the movie never makes it that clear).
Real Life: We're not sure when this Engineer visited Earth to drop his genetic bits everywhere, but there are massive problems no matter the time. First of all, we have no idea how Engineer DNA + Black Goo = working human cells, but whatever. Our real problem is the utter failure to understand how evolution works. Every living (and dead!) thing on planet Earth shares DNA with a common ancestor that thrived in Earth's infancy. That tree over there? You're related to it. A T-Rex? It was your bro. Michael Fassbender? Yes, your instructions are 99% the same as his.
Okay, so maybe the Engineer is meant to be that common ancestor from billions of years back? Well then why did we have trilobites, and dinosaurs, and saber-tooth tigers, and Neanderthals? Do all species share Engineer DNA? No, that's impossible because we already saw the ridiculous "100% match" with humans. So was the point was to seed humans specifically? That also makes no sense because humans could never have evolved in the way we did without a series of cosmic accidents taking place, such as the KT extinction event and other stuff beyond Engineer control. So let's say the Engineer wasn't the common ancestor, but instead imbibed the goo around the same time he inspired all the weird star maps 35,000 years ago. Well then where did our cousins, the great apes, come from? We know we evolved alongside other primates; the proof is in the genetic pudding. So just... what... brain.... exploding...!