The Libyan program recently discovered was far more extensive than was assessed prior to that.
Fortunately, President Kennedy and Robert Kennedy disagreed with the estimate and chose a course of action less ambitious and aggressive than recommended by their advisers.
There's a long record here of being wrong. There's a good reason for it. There are probably multiple reasons. Certainly proliferation is a hard thing to track, particularly in countries that deny easy and free access and don't have free and open societies.
But the most important thing about that story, which is not often told, is that as a result after the Cuban missile crisis, immediate steps were taken to correct our inability to collect on the movement of nuclear material out of the Soviet Union to other places.