So they were wrong in their hypothesis that these 69 sites on the genome are related to intelligence. This does not mean that other sites on the genome aren't related to intelligence.
On top of that, the three gene locations that did seem to have a stronger correlation weren't involved in development of the nervous system.
So they really don't have complete knowledge of this extremely complex system. Not surprising. Time to review their assumptions, and come up with a new hypothesis to test. They still gained knowledge (what doesn't work), it's just not the knowledge they were hoping for.