I successfully met a water spirit in 3.50b2 but I had to try two different locations before it worked. I'm not sure I was on the right kind of rock the first time.
Thanks for the follow-up, Korvi. Haven't heard of Plotinus nor got the save, but it seem there's no reason to suspect a bug.
Spirits are not automatic beings, and as every area and territory has got spirits of its own their moods or behaviour is not universal to the whole game world.
Plotinus, if you happen to spot this, feel free to send the save nevertheless so we can confirm.