Sorry about your troubles. A stony bottom is never a good thing, and usually requires a good, thick layer of clay put down in lifts and compacted to stop it from leaking. One crack in that rock could be connected to many others down below.
Have you considered instead a large rubber liner? It may be an expensive initial investment but almost guarantees the pond will hold water.
I came to that conclusion and have all the costs for a liner. I was ready to buy a liner at a cost of over $60k installed but met with one more contractor in my area that builds ponds locally out of complete chance. (or a prayer if you ask my soon to be wife) He convinced me to try and dig out the area we think is the problem in the bottom and re-pack with some good material I found on my property. The cost for this is pretty reasonable for what is planning to do, but this outfit has mine-sized earth moving equipment at the site I visited.
We will also be cake layering polymer as we build up the area and then pull a final coat on the entire bottom surface.
My previous contractor relied on me to figure out what the problem is and how to fix it, not his expertise or help from a qualified source. I fired him and now have to deal with those consequences.
