From what I see that is a lot more water loss than simple wicking or absorption. It looks to be a leak. It really could be anything though, and possibly even a sand/gravel seam that was missed during construction.
If I were you, I would pump it out a bit at a time, using a little pond dye or simply stir the bottom if you can see where water is going. The most likely candidate will be the junction of the dam to pre-existing soil. If no core trench was dug, then any debris such as gravel, topsoil, etc could make an easy exit path for water. If you are able to locate the leak, you may be able to get the builder back out to do something about it.
You are lucky you don't have fish to worry about, fix the leak first.
Another option is to use your available good clay to line the pond once empty, and rent a compactor and re-compact it. If you can find or rent a tow-behind sheep's-foot roller, you can drag one of those with anything with sufficient power and traction.
