When the pond was renovated and deepened, I bet the original clay liner was breached. In areas where soils are suspect, it's a common practice to line the entire basin with clay, if available.
Years later, when that pond is renovated, if the earthmover doesn't realize the pond was sealed with a clay liner, it is easily perforated, especially if the desire is to make it deeper.

Teach a man to grow fish...
He can teach to catch fish...