How did the aliens who sent us the message even know the human genome? It's implied the message was a reply to the Arecibo message, but the Arecibo message didn't contain the human genome, just the chemical formula for the DNA base pairs (the Human Genome Project wasn't even finished at the time the message was sent, or even at the time of the film). In fairness, the second movie demonstrates that they've visited our solar system in the past so they might have probed Earth in historical or prehistoric times.
Why does Sil need a cocoon? Cocoons are used by creatures like butterflies that have an adult form that's very different from the immature form. Sil doesn't (apparently) change any more between child and adult stages than a human does, and we don't need cocoons so neither should she. It's made worse by the fact she's a shapeshifter so she can change her morphology dramatically without needing a cocoon anyway. And during the cocoon stage the creatures are immobile and therefore vulnerable (Patrick's offspring in the second movie would have torn the protagonists apart if they weren't conveniently all in cocoons when the protagonists invaded Patrick's lair). The whole thing seems to be biologically unnecessary and a survival drawback.
Humans don't need a cocoon to grow from a child into an adult, but Sil isn't human. Humans also don't have the ability to jump from a pre-adolescent form to a grown adult form. If we did, we might need a cocoon stage.
When they make an organism that has nothing but pure alien DNA and it grows super-fast and they have to burn it, what the heck was it metabolising on? There didn't seem to be any food in the chamber it could use to grow.
External heat or an internal cellular splitting process? But they don't follow conventional biology rules.
Being somewhat insectoid in appearance, there's even odds that they are cold blooded animals. What does that do to your heat output equations?
Could that's the pure and natural state of the SIL species when spawning. The budding SI Ls burst forth and devour all they can in order to grow and thrive; it's the most determined alone that thrives. Could be also how the SIL species lives on, it has to bred hybrid offspring, so that its progeny don't devour everything in sight.
Why does Sil's alien form have nipples? Her young seems to be able to feed itself from birth, so it doesn't make a lot of sense for her to have them (aside from maintaining fake breasts as part of her human disguise).
Because she's a Half-Human Hybrid. They're a side-product of her human genome. Her alien form isn't what the aliens "really" look like, even if those who sent the data used their own DNA, but a combination of the human and alien traits.
Just as pertinant a question is why do human men have nipples? We can't breastfeed! Obviously these are just useless genetic leftovers we get from our mothers' genes. Likewise with Sil's alien form - though useless, her hooters are probably just a genetic leftover from her human form.
Something tells me you need to watch Alien 3, which was made three years before the first film, but Patrick was an infected, not a true hybrid, which explained some of that. Or the creators of the second film didn't give a care.
The three minute pregnancies in human women from Species II, with the victim's uterus plumping up like a water balloon in seconds, apparently because a 3 minute pregnancy in a normal human wasn't insane enough by itself. To spare a lot of digital ink, let's just say that a (admittedly amateur) calculation I did had the alien fetus putting out over 900 kilowatts of waste heat at peak growth rate. That's enough to boil several kilograms of water per second, when the average baby only weighs a few kilograms. That's not a fetus, it's a self-cooking meat product. Sil's body might include some sort of mechanism to keep the fetus from cooking itself, but the human body has no such thing. Even if we handwave the fetus survivability issue with Bizarre Alien Biology somehow, there's the absurdity of the victim still being alive when the Chestburster emerges, when she just had ... well, I'm not sure exactly what effect having a 900 kilowatt heater jammed into your uterus would have on your internal organs, but phrases like "steam explosion" and "bubbling organ stew" come to mind. Even by the typical standards of Hollywood Science this is an exceptionally bad biology fail. It's especially offensive because you could easily make the gestation period much more sane while keeping the horror factor justfine and there are a lot more plausible ways of solving the "why not just abort the alien baby" problem, including one that both has real lifeprecedent and isplentydisturbingenough.
Most likely timed so that we could have a Birth/Death Juxtaposition effect with Mommy #1's birth cries being framed with Daddy's orgasm cry as he turns little sister into Mommy #2.
The insane asylum guy's theories about the aliens in Species II are ridiculous. First off, he says he can tell the Mars virus fossils in the meteorite came from another galaxy because it has a form of carbon in it that can only be found there (and he gives a completely inaccurate figure for the distances to the Magellanic Clouds while he's at it, assuming that's what he means by "the Magellanic galaxy"). But that kind of carbon would only be present in the initial seed viruses the aliens dropped on Mars, all the rest of the viruses would be made entirely from Martian carbon. So either we got phenomenally lucky and the meteorite just happened to contain a little of the seed virus (which would be an extremely improbable coincidence), or the aliens would have had to deluge Mars in such ridiculous quantities of that black snotty stuff it would pretty much defeat the whole idea of using a biological weapon (you can do a lot of damage with small initial quantities). Also, since the aliens would have to have a presence within a few dozen light years of Earth to pick up our radio signals it means they'd have to be an incredibly vast and powerful civilization. If guys like that wanted to wipe us out they'd have much more effective ways of doing so than sending us a blueprint for a bioweapon and hoping we're stupid enough to create it and allow it to escape into the environment. That kind of thing only makes sense as a poor man's weapon, used by a civilization that doesn't have the resources and/or technology for anything more effective. There's also the matter of why, if they wanted to kill us and they've been in our neighborhood for billions of years, they just sat around all that time until we developed a technological civilization instead of pre-emptively ruining Earth's environment before sapience could evolve. And then there's how unlikely it would be that a virus designed to infect billions of years dead Martians could infect a human, drastically alter his biology, and produce something other than a corpse. Well, the guy WASin an insane asylum and even if he was sane and intelligent he was probably speculating about stuffoutside his field (and no, there's no way I think the writers of that script were clever enoughto do that deliberately).
Considering just the first movie, you can cast the aliens as trying to be helpful("randomly following advice you get from the internetspace is a Bad Idea"), if you assume they value individual life less than the average American(of course, they could have just as easily been trolling). As for the No Biochemical Barriers thing, convergent evolution gives the writers a handwave.
How come the gestation time for Sil was so much longer than that of her son? And how come he matured quicker than her?
Sil was created in an artificial womb, which could have explained why it took a few days for her to grow. Her son grew inside of her womb, which explains the fast gestation time (and probably, the non-artificial birth would have allowed for the accelerated growth time).
Also, Sil was created from a human egg, which was merely fertilized with alien DNA. The son came from Sil's egg, which would be alien in nature, and therefore not nessisarily programmed with the same development timing.
So they put cyanide into Sil's chamber to kill her. Why on earth didn't they just have a vacuum pump to make her pass out first? It may not have worked, but if it did they could have dispatched her however they wanted. Why didn't they have that nifty fire thing they had at the other lab?
But who amongst us would admit to be willing to torch a seeming-human little girl?
Why does Sil need a cocoon? Cocoons are used by animals that dramatically change their shape between the juvenile and adult form, like butterflies. Something Sill doesn't do. Not to mention that she's a shapeshifter anyway; she rearranges her body without needing a cocoon multiple times in the movie.
remember that Sil had rapid regeneration powers, hence why she could survive the birth, while the female astronaut didn't. Though, this brings another Fridge Logic of why the female astronaut didn't turn into a hybrid while Patrick did...
As they were digging that Absurdly-Spacious Sewer under the hotel, not a single survey detected the GIANT CAVE SYSTEM?