Sadly "stuff happens" in the developmental process. One of my stallions - we found out after the fact - had a developmental problem. His intestine was complete, but something in the way it was formed allowed it to torsion easily and we wound up in colic surgery late in his yearling year. The vet was able to stitch it up and create some adhesions - which he said would either work for him or would do him in. In this case it worked, he's 10 this year and has good healthy babies out there. The vet initially suggested putting him down but was creative and such a skilled surgeon.....we owe a lot to him. I guess my point is that I wonder how many of these issues are out there and go undetected depending on the severity. Your colt unfortunately was unable to survive his, but I'd guess there are many with less extensive abnormalities who live - or who die young for unknown reasons.
Jan