Scientists Probe Sounds In Cuba That U.S. Diplomats Complained About

I guess it wasn't that particular sound. Or perhaps what they heard was similar to that and what effected them wasn't within their conscious hearing...

Snopes ran a good article on this and I will link it. It is highly unlikely that it is a sonic weapon given the limitations of such weapons and the fact that it's far, far more likely that the underlying cause is a stomach bug or food poisoning. The location and its former isolation from the US make it potentially problematic for visitors or staff and their diet, much like we see with soldiers or deployed military serving overseas on deployments - ya just don't want to eat at any random passing food cart!
Lastly, there can also be other exposures that we're not aware of that the Cubans have developed immunity to, like a mould or fungus.
https://www.snopes.com/fact-check/do-sonic-weapons-explain-the-health-diplomats-cuba/