The whole planet?
Don't knock it, I liked this movie. It explained his psychic visions, which most movies with similar premises either don't explain or never deliver a solid answer on if the character was right (Take Shelter). BUT.... did the entire Earth get taken over by the synthetics? If so, why don't they have a planet-wide army beating back the humans? If not, why wasn't there anywhere for the humans to run to without having to go to Mars? Was this city the only synth city?- It is possible that war 50 years ago took great tool on both sides and they numbers greatly diminished. (humans made first strike so androids were not prepared for original war) We don't know how advanced are mars colonies. Limited resources may have somewhat limit how much humans could reproduce to increase their numbers. It is likely that androids only knew how to do basic maintenance and can't build more of themselves. (why would they be given this knowledge in the first place if there was fear of the rebellion) Doctors weren't able to do anything for Alice while Miles was able to save her with rather rudimentary equipment (He probably wouldn't even have to use Peter if other android power source was available) As for why humans didn't run away to other part of the planet. Probably human and android populations were intertwined everywhere so there was no separate territories for each side 50 years ego.
The train at the end
Is a cool concept, but the pop-up/pop-down bridge and explosion to cover the hole will be dead giveaways leading straight to the underground base. There's still going to be rubble underwater denoting the holes to follow. Even if they used a few fake holes, it isn't going to last long. And that's assuming the invaders didn't 1st scan and record the whole planet. If they did, especially if they have observation satitiltes taking pictures, they'll beable to follow the trains.