With the good clay you had, the contractor may have done only about a 1' thick clay blanket to seal a pond with a depth of 10' or less. With good compaction in lifts, and under NORMAL pond conditions, that would be capable of perfect sealing. With plenty of good clay, he may even have made a clay blanket of 2' or more.
The problem is, many crayfish burrow down 3' deep, and some may burrow as much as 10' deep!
I really think it is a "creature" problem when you say the pond is fine for weeks and then suddenly drains.
I am NOT an expert on eliminating the crayfish, but we do have experts to help on that problem.
Can you trap or catch a few so we can get the correct species identification? Also measure their size on a few specimens.
We may need to target them with the correct size and type of predator to eliminate them.
The other option may be to outcompete them. Perhaps there is a non-burrowing crayfish you could stock that would reduce the population of the darn burrowers?
Good luck fixing your problem. I hope you get some better advice from our actual experts on this topic.
