It's not really mistakes.
It's not mistakes at all.
A mistake is like in Alien 1 when they assume that the guy who's been infected by the facehugger is all good, and so they're like "Oh shit, man we thought you was dead but everything is okay now so c;mon out of containment." AND THEN AN ALIEN BURSTS THROUGH HIS CHEST AND KILLS EVERYBODY ON BOARD MINUS ZUUL AND THE FUCKING CAT.
That's a mistake.
In Prometheus, here's how it happens:
A supposedly supernova traversing intergalactic biologist who is, apparently, afraid of a 10,000 year old mummified alien (Despite this discovery), taunts an obviously unfriendly and harmful alien snake creature by prodding it until it attacks him, killing him and causing his friend to turn into a zombie who kills an untold number of people on board the ship.
There are no mistakes in prometheus. Just stupid decisions by stupid characters over and over again. Besides David who is, at least, kind of entertaining. And Lizbeth the Astronaut Salander who does a pretty good job, IMO.
EDIT
JEsus even the super intelligent space creatures are idiots. Why does Super-Powder space alien chase after Lizbeth in the final(ish) scenes? Why doesn't he assume she's dead? What point does it serve to kill her when you're originally planning to kill THE ENTIRE HUMAN RACE. IF he knows she's alive by some sort of space cognition, SURELY he knows that the giant space octopus is also alive? Surely? He's a brilliant space alien.