Question: Couldn't the ragdolls have run away? Why did they have to fight the machine when they could have simply left?
Question: It was shown after 9 woke up, he lacked a voice box, which 2 had to make for him. But how did the other Stitchpunks (minus 3 and 4) get their own voices?
Answer: The inventor did, he died before he could finish.
Question: Why were the dolls sent out after the scientist made them? Why didn't they stay with the scientist so he could explain everything?
Answer: They were sent out into the world to create a new world for themselves. Every time the scientist created a doll, he transferred part of his soul into the doll bringing it to life but leaving him weaker. After creating 9 and transferring the piece of his soul into 9, he died so they would never have found out what they were created for.
Answer: The machines could have followed them anywhere, the only way to be free is to destroy them.