i had this problem , we couldnot at first find the hole until we completely emptied the pond and we then found the hole.It Turned out we had a couple of jholes that were about an inch big, it looked like that birds (heron) had been going in the pond.
We ended up getting a new pond liner.
What we do was put a layer of sand on top of the old liner and put the new one on top.Mind you it did take about 3 to 4 hours to fill the pond up again.This is because hubby made the pond bigger.
And no it was not hubby who mad ethe hole in 1st place

Yes usually when the water stops leaking then the hole is above the level of the water, but you may have several holes. You dont need much of a hole to loose a lot of water and they are not easy to spot. Conserve the water if you have to empty the pond, in paddling pools etc. " other reasons for holes are piercing the liner? Did you break any ice over the winter? or is there sharp stones under the liner which are not covered with enough sand etc before you lined it? Or did something fall in Like a large rockery stone? In a new pond you get a reduction of water as the liner fills out with the weight of the new water, but this only happens in the beginning.