[Alan]

What the hell made Dr. Shaw believe that the glyphs on the walls were invitations to visit the protohuman planet?
They all pointed to the same system, which makes it a map. These were scientists the same way as cryptozoologists; they have a background, but they also had an belief, they just happened to have been right.

Why did Dr. Holloway come back to life with superhuman strength and a desire to kill his former colleagues?
He was infected, not made a host. The black goo was the biological weapon, the xenomorph was just one of its iterations.

Why did David even want to contaminate Dr. Holloway's drink with that weird alien goop? He didn't have a damn soul!
He asked Holloway how far he would go for this discovery. It was the only advance they had yet, thinking everything else had been dead for two thousand years.
What I really want to know is why you think it would have been less stupid if he did have a soul. Was he supposed to be a real human being and dot FOR THE EVULZ?

When an incredibly long, heavy object is falling to the earth from above, why run the length of it instead of simply dodging to the side?
They actually DID run to the side, but they also had to run away or they wouldn't have made it on time. If she didn't run to the side you wouldn't be saying this part below
After she tripped, Dr. Shaw was able to simply roll out of the way of the protohuman ship as it came crashing down; she could have done that the entire time, and then she would have had longer than 2 minutes of oxygen left by the time she came to.
Proof she was running diagonally, as the bird eye shot also showed.

Speaking of her dodgy survival, how did a fucking rock keep the several-ton ship from falling on top of her? It had no trouble crushing everything else in its path.
That WAS the only plot hole here. Everything else is easily explainable.