I may not know much about kidney stones, but I've had multiple bladder infections and risked kidney stones before when I was 18.
One thing I can say, I'm not going to be 100% positive on it, but if your son drank cranberry juice (lots of it) check into the effects of the oxalates(in cranberries) and the calcium(in your urine) building up to possibly form kidney stones, the last question on the linked page will be helpful if that's the case.
If not, the doctors could be just concerning about kidney infection due to the bladder infection which can get very serious. But no matter what there is always a possibility even at a young age to have something that serious.
(Doctors told my fiance he was too young to have had an ulcer when he was 17 and they were wrong stress and body stress can really cause a lot of problems even when you're young)
I hope this helps a little and that everything is alright though, best of luck to you and your son :)
Were you able to get the results of the scan already?
Kidney stones may occur at a younger age but very uncommon. In these age groups metabolic disorders need to be ruled out like increased oxalate levels in the blood. I do not think this is true in your son's case. Urinary tract stones are usually associated with abdominal pain which is sudden and severe in onset. Crystals may also be noted in the urinalysis .In severe cases, kidney stones may present with dull back ache, fever and chills.
The CT scan will be able to determine involvement of other structures. Also, a hemogram of the blood cells may help. The appearance and size of these red blood cells may help determine if there is kidney involvement or not. Hematuria may also be a manifestation of kidney inflammation. Urine protein levels my need to be ascertained.