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This is a short story a friend of mine told me about some time ago.
It was written by Philip K. Dick. It was about an AI which controlled US defense system The AI decided that the main threat for humanity was something ridiculous (I don't remember what exactly it was). Because of this, the government/scientists concluded that the AI was broken and decided to turn the machine down.
The plot twist at the end was that
the AI was right.
It's the short story "Holy Quarrel". The protagonist is a computer maintenance guy who is called by the secret service to decide whether a defense computer who is attempting to scramble SAC bombers to destroy a US city has gone crazy or is actually working as intended and has detected a subtle plot against the US. The computer is jammed to prevent it from actually carrying out its attack until they can decide whether it's working properly.
It turns out the computer has gone religious and has decided that a vendor of trinkets and candy is the anti-Christ. They decide to disable it. In a typical plot twist, the computer was right, but by the time they find out, the sample candy has started self-replicating uncontrollably and it's too late.
