Humans are basically inert to each other due to being "one-dimensional". But what if more people try to grab the same object or use the same device? Would an item blink out of existence before your eyes or float in the air if someone else took it? Or does everything exist for each person separately? If yes, how could people be able to leave notes for each other?
Through the narration it is revealed that the Kent Lighthouse was a part of the subnet before it was actually buried. Possibly always. But in the end its topmost part actually emerged into the regular world. What just happened there?
In the final 10th game you get to revisit the lighthouse digouts once more and find that walled doorway as it was in the 2nd game. But wait - didn't you blow that walled doorway back in the 5th game? How come it's intact again? Did you travel back in time? If yes, what's all that red goo (sand?) doing there? This looks like some seriouscontinuity error.
Why did S.H.I.V.A. give Murtaugh the power to mess with Karma? Being an AI which surpassed human intelligence wouldn't it properly assume, that Mur's karmic portals would mess up the fabric of the Subnet i.e. S.H.I.V.A.'s body? Or did S.H.I.V.A. do it on purpose as a way to further evolve?
What's with the "holy usher - disciple" conversation note in the final game? It makes little sense. First of all it's the only case in which someone enters the Submachine willingly. All other people mentioned in the series already kind of were inside from the start. Second why and how do you "ready yourself" for Submachine? Despite mentioning it a few times it doesn't really require some special training. If you know how to use items and are literate enough, you should've no problem faring through the subnet. Whoever the mentor is, they treat the discpile like their journey is something special, some Rite of Passage or what. But countless people are already traversing the subnet and while some do have trouble, most of them kind of get by with it. There's no implication, their endeavor is supposed to transform them in any way. The note seems just too melodramatic while seeming to hold no meaning at all.
