If they accepted every perfect candidate that applies to their college they would have to build two-three new colleges just to fit those applicants alone. Your son a very high status in my book and I’m surprised as well, but you’ve got to look at the college process holistically and understand why they chose their decision.
If you’re really agonized by the decision, you can call them up and they will tell you the specific reasons to why they didn’t pick your son.
Wishing you good-luck!