When 9 wakes up at the start of the film, there is only one villain left. 7 kills it before any other villains emerge or any heroes die. There was only one villain stopping the characters from getting a happy ending, and just one of the 9 main protagonists easily defeats it.
When 9 foolishly activates the fabrication machine, he accidentally dooms most of the cast. If he hadn't done that, none of the stitchpunks would have died.
There are still withered human bodies lying around; presumably the machines' gas not only exterminated life down to the microscopic level but stopped all biochemical processes in their tracks. Pickling gas, perhaps?
Killing all the microorganisms would make stuff wither a lot slower. In fact, this is how pickling works.
So, the Fabrication Machine/BRAIN was created and used to make more machines. But why in the world would it have a place to put something that could suck out one's soul? Why would you build a machine with that function—wait. This machine was used during a war. So, any P.O.W.s or anti-war protesters might...Oh God.
This could've been how the war against the machines got started. The movie claims that the Fabrication Machine turned against humanity because it was corrupted by the military, but it had to get its power from somewhere. Say people figured out what happened to the missing anti-war protesters and, naturally, they had a problem with it.
A Wild Mass Guessing for 9 suggests that the dolls' purpose was to be soul-sucked and then have their souls released into the sky so life could be restored to Earth. If that's true, then at least five of those dolls were born just so they coulddie. And not a nice death, either—a horrible, painful, terrifying one!
As if she wasn't terrifying enough already, The Seamstress becomes even worse when you stop and think about how she catches things. She literally sews you to youself, effectively binding you using your own skin.
One might have to get over the warm and fuzzy feeling of the ending before realizing that the survivors are doomed to live with only each other until they break down. Even if that was life raining, a few micro-organisms would be no comfort in an otherwise empty world. This isn't an aversion of the end of the world; it is completely played straight in spite of the inventor's best efforts to create new life.
You have to start somewhere. Fortunately, the Stitchpunks are immortal and can afford to wait.
Not so much to do with the film itself but freaky nonetheless. 9 is played by Frodo of the Nine Fingers, who is part of a Fellowship of nine and has the word "nine" tattooed in Tengwar on his hip. Coincidence?
7 wears a bird skull. What does she slay? The Beast with a cat-skull head, in the style of 'Usually peaceful herbivore/omnivore defeats the scary predator.'