There are worms that are known to burrow in silicon. I just heard a presentation about some at MACNA. A large tank in Steinhart Aquarium had this problem. Worms burrowing and parrot fish eating silicon, created wholes and leaks in a very large tank.
Now, I'm not sure if this is what really happened to you. I'd guess you would have found the worm in its burrow in the silicon if it is the case.