That these super advanced beings capable of interstellar travel, somehow had their ship break down at planet Earth, without any regard for the impact their presence would cause, and with a seemingly ignorant appraisal of human psychology and greed.
That they allowed themselves to be imprisoned in a ghetto when they had weaponry and numbers to wipe out the human race.
That they bartered their weaponry for cat food...
That humans and the aliens could communicate with ease, yet there hadn't been any kind of sophisticated cultural intercourse.
Ah so you didn't understand the film, where it was coming from and what it was getting at. People no matter where they are from in desperate circumstances can end up living uncivilisaed in squaller. This has happened many times in human history, it was using alien in this case. The plight of the aliens was a parallel to the plight of millions of humans who have become refugees and all social order breaks down and live in squalor and refugee camps.
They had no use for their weaponary, and these were just a worker class of the aliens. There were the much more intelligent ones among them however.
The communicating thing is a non issue. They'd been there for 20 plus years, and had been kept in the camps.
That they had immunity to all our nasty microbes, and we to theirs.
That is nit picking to be nit picky and isn't a plot hole or a flaw on anything. There isn't some rule in nature that alien microbes automatically are deadly to people from another planet. There's nothing to even say they'd be similar types of life.
We treat other humans that badly and worse? Why not treat broken dying aliens, when we want their technology and weapons how we treat other humans? Part of where i think you missed the central theme.It was just too ridiculous to think humans would realistically treat an alien race so badly, when the possibility of ten thousand motherships appearing some time in the future was entirely possible.
That the protagonist somehow become infected with a compound that transformed him into one of the aliens.
This is just not buying into the film and not a flaw.
That the evil scientists didn't treat the protagonist more humanely, alienating him to the point of his escape.
The entire scenario was absurd.
Nopes you just didn't buy into the film and so there for didn't understand the premise, couldn't sympathise with the aliens and their situation, put it all in the context of human refugees and second class citizens through out the world and history. There for just label everything stupid just because you didn't get it. Which there's nothing wrong with.
Films are subjective, didn't like, cool whatever. However your criticisms are invalid justifications for just not buying into it. Also having not seen the end of the film you missed out on a lot of answers and resolutions to questions and the themes of the film.