I've read about this before, though I heard it rarely happens.
The interesting part is that the problem happens when you DON'T use your lens. Fungi thrive in dark damp place. So storing your lens in a damp place could be a problem. This is why when I got into photography, I started collecting those silica gell bags with "Do Not Eat" and "Throw Away" warnings on them, as they help absorb moisture.
Did you check your lens, the same way the guy did? You can open up the aperture and look for signs of fungus. You're looking for spider-web looking crud. From what I gathered online, you can kill them with light. Either fire up flashes on them, or using flashlight. You probably have to leave the aperture open.
I don't know if Nikon warranty covers it.