The children are born inside of the orphanage and each mother is not allowed to ever see them again. As Nine is born, as he doesn't know his name and is only ever called by a number, his mother is allowed to hold him for only a moment before he is taken away from her forever.
Nine grew up with other babies and children his own age and several that were born 18months later to the same women.
They begin training these children as a government operation unknown to the public. They are raised government trained. They are taught the masters of disguising themselves, fighting, sharp shooting and many other things.
This one is just as good as the Ninth Orphan, just not sure why it came second when it was the beginning of their lives and it might had needed to be first.
Either way, it works out great and happens to be a wonderful story!