Stupidity: In 300 years, in an empoverished world full of people hungry for techs, nobody ever tried to remove the ship from a small pond barely 15 feet deep, and everything inside seems intact. It is mentioned that few tried because the technology is hard to sell being unknown (which is laughable), but surely some would try to strip the ship for alloys, and certainly the lights and monitors wouldn't stay untouched in a world based on scavenging. For 300 years and so close to the city, even.
Stupidity: Cyborgs have amazing jumping capabilities, but the assault on Zalem basically failed because the whole platoon of United Republics of Mars blindly shooted at the defense ring with puny rifles and never trying to avoid it (and they were fully aware of its presence). The novelization at least makes more sense since they have better weapons and it's the tube giving out that wipes them out - here, it happens after it already killed everybody except Michelle Rodriguez.
Stupidity: She does not go through with the plan, but the idea that Alita would for no particular reason literally rip her heart out, ask Hugo to sell it, and then think about looking for "a cheap replacement" (when Hugo has almost a million bucks collected anyway) is really getting your priorities wrong, especially considered that in the movie, cyborgs seem to have a circulation not too unlike humans', so without heart she'd not be able to even walk.
Stupidity: In the wanted poster for Hugo (he's the only person named "Hugo" in the world, apparently) his bounty for one murder is 30,000 credits, 50% higher than the notorious villain Nyssiana who slayed 7 people (and who knows how many other felonies). Obviously the system is rigged, but one wonders why do they even bother to keep appearances up when murders obviously not committed by a person (Zapan's Damascus Blade is one-of-a-kind, so at most they could have pinned the murder on Alita who shares the tech...but who cares since there's no real law-enforcement or trial?) can just arbitrarily be pinned on others with whatever bounty.