1. After the attempt to hack the computer-based spaceship where 98% of humanity resides is successful, we learn that this man, Frontier Settler, has hacked the ship over 100 times. Now, given that they presumably have super-futuristic technology, you might be wondering why Deva (the name of the spaceship) have not heavily beefed up their security to keep this from continuing to happen. The film refuses to answer this.
1a. You might also be wondering exactly why people choose to STAY on this spaceship if it is so vulnerable to being hacked, even if by an incredibly skilled hacker. This is something else the film doesn't answer.
2. Now instead of having one of their best agents lead the investigation to the whole Frontier Settler deal, they decide to have a third-class agent lead the operation and an S ranked agent, already stationed on Earth and knows the place well (which Frontier Settler is believed/known to reside), to simply function as her minder. It is never entirely clear why this is the case; for a few reasons the S ranked agent- Zarik Kajiwara- is not held in high regard, but clearly his work is still respected, if he is allowed to hold such a high ranking.
2a. Exactly how the whole ranking system works is never clear. Is S a special rank in some way, or are, say, 1 and 0 higher? What is considered a "high" rank? None of this is really explained.
Three. Our main character, Angela, is supposedly an incredibly skilled hacker. One would imagine that this would mean that she would be familiar with Earth jargon and basic computer knowledge, which would logically originate from Earth. Despite this, she is completely unaware of very basic facts like that sand is not exactly tasty. (No, seriously, upon reaching Earth she tries to eat sand. I THINK this was supposed to be humorous, but it was just stupid.)
4. Angela's stupidity doesn't stop there. No, Zarik need to inform her that utilizing her mech to traverse Earth would likely draw Frontier Settler's attention. Now, I am completely aware that savant syndrome is a thing, but it is taken to such a degree here that it simply boggles the mind.
5. Now, since it has been pointed out that being in something as conspicuous as a mech would draw attention, you would THINK that Angela would change to non-conspicuous clothing to more effectively blend in. She doesn't do this. For reasons that I am completely unclear on.
6. Somehow, to make matters worse, this doesn't draw Frontier Settler's attention. Let's be clear here. This is a super-advanced hacker that has managed to hack into a spaceship over a hundred times, and somehow he doesn't have the resources (despite having robots he can deploy) to spot somebody that clearly isn't from this planet and sticks out like a sore thumb. Ok.
7. A noted aspect of Zarik's character is that he's afraid of heights, yet later we see him on top of an abandoned building stringing his guitar. It is never explained why this would be necessary or desirable for him.
8. By the end of the film, the only thing resembling a character arc Angela has is that she gains respect for the human way of living. Things that have happened to her since she arrived on Earth include: Nearly getting raped, having her mecha destroyed, and experiencing annoyances such as exhaustion and hunger. Yet somehow talking to Zarik about the nuances of their job totally changed her perspective.
9. It is explained in the film that human consciousness was transferred into data. Don't expect the movie to explain how this worked, or how it was even possible, though!
10. After Angela crashes on Earth, she fights a giant centipede monster... thing in that mech I mentioned. This would actually be a good explanation as to why humans in general left Earth and wanted to become digitized, particularly if there are other predatorial species. This is never explored.
There is more I could have put here, but honestly it isn't worth the effort. Man this is a bad movie.