There are these four theories concerning the soul:  The soul comes from propagation.  The soul is created new in the case of every individual.  The soul exists elsewhere and is sent divinely into the body of a man at birth; or lastly  of its own will, it slips into bodies. We must not affirm any one of these rashly. Either the catholic commentaries on the divine Scriptures have not yet given this question the explanation and enlightenment that its obscurity and complexity deserve; or, if it has already been done, the book has not reached my hands. [On Free Choice of the Will, III.xxi, p. 133f]
Several thoughts come to mind. First, it is surprising to me at first glance that this might have been unclear to St. Augustine at any time in his Christian life, but maybe that’s being a bit too unfair. As a Protestant I learned that there were two theories about where the soul comes from, corresponding to the first two mentioned by St. Augustine above, but it was never exactly clear which of these one must hold (if it was even something that Protestants would consider that important). I guess I would never have imagined the question being as apparently difficult as Augustine does, but there you go: we stand on the shoulders of giants, right?
[For those who might not know, the Catholic Church teaches (§366) the second of Augustine’s theories; this is what St. Thomas taught, too]
Secondly, it’s worth noting that St. Augustine fully intends to submit to the teaching of the Catholic Church on this point. He has no intention of jumping to a view of his own apart from what the Church says. The problem he faced was one of ignorance: he didn’t know what the Church taught about it, but it seemed to him that if the Church hadn’t yet spoken on the subject, it should do so. St. Augustine, we see, was by no means one to suppose that he could get along just fine with just his Bible. No. He understood, and we need to understand, that when we come to the Bible, we must read it within the living tradition of the whole Church. We don’t read it within the tradition of the Presbyterians, or of the Baptists, or of the Lutherans; we read it within the tradition of the Catholic Church. That means that if our interpretation of the Bible contradicts the teaching of the Church on faith and morals, then we have made an error in what we think the Bible says. Period. St. Augustine was a faithful son of the Church; it seems clear that this was his view as well.
Thirdly, St. Augustine understood that doctrine develops. Over time, the Church’s understanding of the Faith grows and becomes more clear. In our passage above, the saint makes it clear that it was at least possible that the Church had not yet spoken on the matter, and that he hoped that She would do so. I don’t know if She had done so by his day, so that Augustine was simply uninformed on this point, but She has spoken by now, as I pointed out above.