A few questions (spoilers)
1. Why did the machine want the souls of the dolls?
2. Why was there only one "beast" left in the beginning. Didnt it seem as if the machines had won the war?
3. Why was the main machine turned off? Did it turn itself off? Did someone turn it off? If so, doesnt that mean that it was defeated?
4. If the circular thing was so dangerous, why did the scientist leave it for 9 to find?
5. 9 said that 1 knew something, usually when that happens in a movie, it is revealed later on what the character knew. So what did 1 know?
6. Why did 9 come to life after all the other dolls?
7. When the machine fell off the bridge, the doll that it was holding told them to go back to room 1. How did he know that, had he know it all along? If so, why didnt he go back to that room earlier?
8. 9 knew exactly what to do after seeing the scientists hologram, even though it was a very vague explanation. How did he know?
9. 9 was against destroying the machine before releasing the souls. Why didnt he think that destroying the machine would release them? How did he come to the conclusion that destroying the machine was dangerous to the souls?
10. Did the scientist know that in order to make rain, his little round thing would need the souls of his creations? Did he create them to be sacrificed? So does that mean that he predicted that 9 would find the thingy, inadvertently awaken the machine, then the machine would take a few souls and then 9 would figure out how to defeat and retrieve the souls? Was he psychic?