So far my favorite example of a bitter internal U.S. intelligence dispute manifesting itself in a very flawed (to say the least) public perception crisis of what was really taking place. Below, the Special National Intelligence Estimate, Sep. 1962:

The one person in the Kennedy administration who believed the Soviets were sending offensive missiles to Cuba was CIA Director John McCone. The problem -- or problems?

1. McCone was on his honeymoon in Paris at the time, not in Washington. His order for daily U-2 overflights in Cuba was overruled by Dean Rusk and Robert McNamara. His suggested SNIE raising the alarm was similarly ignored for the above.

2. McCone was a Republican in a Democratic administration. And GOP Senator Kenneth Keating was banging on about Khrushchev sending surface-to-surface missiles to Cuba, prompting Kennedy officials to suspect McCone was leaking to him.

(He wasn't. Keating's sources were almost certainly Cuban refugees.)

3. The placement of SA-2 surface-to-air defensive missiles around Cuba made McCone very suspicious, as these were not guarding airfields. The manual for the SA-2 was provided to CIA by Oleg Penkovsky, a HUMINT source whose identity JFK didn't even know.

(JFK knew the CIA had a Soviet colonel working for them, but not who or his closeness, via Varentsov, to Khrushchev.)

4. The manual for the SS-4, the medium-range nuclear-capable missile the Soviets placed in Cuba, was also provided by Penkovsky. And that system was judged to be the culprit only after U-2 overflights restarted -- that is, once John McCone got back from his honeymoon in Paris.

Until that photographic proof, McCone had relied instead on his own judgment, the available slate of circumstantial evidence, and information provided by an incredibly high-value Soviet mole. The conventional wisdom was: "The Russians won't do it because they haven't before."

To recap: one of the most dangerous postwar crises the U.S. ever faced -- the threat of nuclear war with the USSR -- might have been more fleet-footedly (or even preemptively) dealt with had the CIA director not run off to be married at the wrong time of year.

And a nice coda to this story:
JFK later told McCone, "You were right all along."
To which McNamara said: "But for the wrong reasons." What the hell did that mean?
McNamara later confessed to McCone's executive assistant, "I don't know. I had to say something."