It’s no different than cars. You can test the thing a million times, but you cannot account for all possibilities. Take a look at cars, for example. Cars are only a fraction as complex as a jet fighters, but despite the battery of tests a car goes through before it goes into production, there is always something that becomes unaccounted for and a recall goes into effect.
I read Chuck Yeager’s biography and he wrote about test flying - a bit different than cars. But yeah, individual systems can fail but the dynamics of the airframe would show its flight characteristics.