I'm going to pointing out non-sense in Prometheus as well which naturally will tie into Covenant.
1. Answer me this very basic question first, why is David an asshole? It's never explained in Prometheus why he is a secret asshole fucking with the crew? Why does he "hate" humans? Why does he do these experiments? How did he know the alien goo would do anything in Prometheus? Why? Why? Why? And, don't give me the stupid, "he's an android, AI's always turn on their creators." Nothing in Prometheus explained why David would turn on his creators whilst simultaneously be obsessed with creating some new life form and torturing his masters.
2. Why would the Engineer homeworld (assuming the leak is true) consist of one city and outerlying forests? They have no other cities? This being the homeworld of an interstellar race of Space Gods and what not.
3. Why do the Engineers have zero planetary defenses to stop David from releasing the black goo?
4. Why do they have no antidote or counter to the black goo which they themselves created?
5. Why would Shaw trust David to do a single fucking thing after the events of Prometheus? Why not just keep his disembodied head to do computing and analysis shit and thus prevent him from fucking about?
6. How does David get a new body after him getting fucked up in Prometheus?
7. Why doesn't the Covenant crew immediately suspect David when he's the ONLY "earth-like" thing on the planet? Did the Prometheus crew (or rather Shaw) send ZERO messages back about their malfunctioning retard android?
8. Why does Shaw even go to the Engineer homeworld instead of going to Earth first, get some Space Marines, and then head over?
9. How does any of this explain Space Jockey and all his alien eggs in "Alien" when David supposedly wiped them all out and created the xenomoprhs later?
10. How is ALL of this kept under wraps by the time "Alien" comes around?
I could go on. Everything I've read suggest Prometheus 2.0" Electric Xenobugaloo. The mystery behind Space Jockey and I guess his now, known race called the Engineers, seemed pretty simple in the originals. Adavanced race creates a biological lifeform to fight in their wars, perhaps even a civil war, species becomes too advanced and wipes them all out. Done and simple with a nice social message. Now, we've got Engineers creating humans with black goo, leading humans to some colony where their Android goes crazy for no reason, they wake up an Engineer who despite creating humans now hates them and tries to kill them, David experiments with black goo on his human masters creating fucked up hybrids, crew member survives everything and decides to best plan of action is to go to the Engineer homeworld, alone, with her crazy droid. Crazy droid then obviously betrays human, kills all super race Engineers, spends decade or so on planet continuing experiments before beacon causes a human crew to show up so he can experiment on them and thus finally create a xenomorph so that it can????
What's the message? What's the point? Why is anyone doing anything in these films?