If you have not figured it out by now, you have a major problem. Ponds that leak, typically leak down from full capacity about 2 to 3 feet or 4 feet max and then the water level stabilizes. This indicates that the water is seeping out somewhere in the upper zone probably due to an undiscovered drain tile, tree roots, or porus soils etc that are close to the side walls.
But in your case, when the pond leaks totally down to only 6" total depth then this means your pond bottom is not adequately packed, or a porus soil/gravel vein is near or close (closer than the expected 2ft) to at least some area or areas of the pond's bottom. Your water is obviously leaking out the pond bottom which it rearly does if a thick layer of good hard compacted clay composes the pond's bottom.
Your contractor/pond builder did a poor job since he knew that gravel/sand veins were close to the pond bottom, the contractor should have taken extra precautions in packing the pond floor. Maybe even spread betonite across the entire bottom worked it into the basin and then compacted. You need to see if he "stands behind" his work and what it would take to get him back to fix or repair the "leaky hole". For comparison, you should also get an estimate from another contractor for this fix.
About the only way I know to fix this problem is to drain it, and excavate with a backhoe or small dozer the bottom deeper looking for sandy or loose soils that are relatively close to the bottom. A backhoe may have to dig test holes in the bottom looking for lose soils and the depth of good clay which may not exist in your case. If no suitable clay is below the existing bottom, then bentonite should be worked evenly into the bottom and compacted. Then as insurance, I would then haul & spread at least another 12" of good clay into the bottom and compact it in layers with sheepfoot roller. It would not hurt to add another layer of betonite to the new bottom top layer and compact the crap out of it again. Betonite if mixed into the soil and compacted properly will work well in your case because it will always be covered with water and the seal will be maintained and cannot dry out. Betonite is less successful when sealing the upper side walls of a pond due to evaporation and chances of dry out & soil cracking increase.
Betonite is a special type of powdered clay that swells to about 10 times its size when wet. This consolidates the soil-clay mix and when compacted forms a water tight seal as long as the "seal" remains wet.
Even after doing this there is no guarantee that when refilled a leak will not occur somewhere in the side walls where sand/gravel/tree roots/ tile are close the the basin walls. Sometimes the cost of fixing a "leaky" pond can be as much or more that the original construction cost. This is why it is important to get it done properly by a knowledgable contractor with lots of experience and a proven track record the first time.
