The edge case is on the developer side, where app developers who create an excessively large deep link information file cause the service to crash on end users' phones.
The only way this would have been found in beta testing for any version of iOS 9 is if a developer had made this mistake while beta testing was underway, and it does seem that there were a few instances where it was reported prior to 9.3 beta testing. Ideally Apple would have built in a means of handling these files if they are too large, but it's hard to foresee all the ways a user or developer will do something wrong. It's possible that even if the crashes were reported in beta testing that the developer who was causing the crash fixed their file, rendering the bug unreproducible by Apple. This would be extremely difficult to find in testing.
Maybe but that doesnt explain why this isn't impacting everyone and people who haven't upgraded yet.