There’s a strong possibility that this movie is the hodge-podge of a number of script revisions, especially considering the changes that happened after Patrick Wanye signed on. Some stuff may have been revised during the shoot as well.
Also, the script is maybe more understandable as a screenwriter just working scene from scene, trying to establish certain story beats without a care for characterization or coherency.
So they wanted to make the story about a “lost tribe,” and people coming across them for the first time. They made them decedents of Atlantis to make it slightly more interesting. So the first scenes establish why they’re still considered “lost,” they kill all outsiders, while also establishing a link back to civilization with Syrene making trips, and the pearls as the MacGuffin. Also, they want the tribe to be noticeably different, hence the bug eyes, but they don’t want the main tribe characters to have them, hence the “missing link” storyline, where they breed with outsiders on occasion.
So then we have Manuel sell the links to Eddie, who gets the idea to harvest pearls directly from the source. Why does Eddie get this idea now? Is this the first time Manual has sold pearls? No, but Eddie just took over his old buyer’s territory. Eddie recruits in a diver, who then recruits in another diver and boat captain. But wait, what about the Atlantis angle? None of those 3 are going to be that interested, or give any exposition about the tribe or Greek history or anything, so they need a “doctor” character, so how does the doctor get involved? Oh, just by pure chance, overhearing them in a bar. And why would any of the three give the doc a second look? Why, make her a woman of course. This could also set up a potential love triangle between the two divers. There’s no forward thinking, or backwards thinking, just writing what’s necessary to get to the next plot point.
For example, if Syrene is making monthly trips to civilization to get other supplies, she’s had a TON of opportunities to leave her tribe, if she wanted. Just go on one of the supply trips with a good amount of pearls, which she knows has value to outsiders, and just never come back. But no, her father suddenly imposes a command to mate NOW, even though if it was so urgent, she could’ve had sex with the outsider from the beginning before they killed him, or slept with someone while on the excursion to the outside world. But the writer wants to establish tension and a love triangle for the end of the film, so the two women in the story are suddenly in love with the same man, no establishing in previous scenes at all.
It’s like with the final scene, where the movie wanted to end on a lighter, comedic note, so have Vic fail to retrieve the chest of pearls, and then pitches a plan to recover the chest ('the coral’s only 50 ft deep, if [the chest] didn’t go over the edge, but even if it did a team of divers could cover the whole reef it in a couple of weeks.) It’s a very Italian Job type ending, and if it was tied to a different movie, a lighter take on a pearl expedition, it’d be fine. The problem is this comes after a series of fights and betrayals and double crosses, along with the extinction of an entire tribe of people, so it’s total tonal whiplash.
Each individual scene makes sense on its own, it’s only in combination with the scenes before and after that the total lack of coherence makes them incomprehensible in context.