Probably just normal evaporation, plus some underlay wicking action. But it's worth checking any folds to make sure they aren't siphoning water out.
I was having an issue with the pond losing about 5 cm per day (call it 2 inches) and then losing almost nothing once the water level dropped below a certain point. I went around finding little low areas where I'd folding the liner over; any place where the liner had been folded "vertically" and then folded over horizontally to hide it was suspect. Found a couple of places where water was siphoning up through the vertical folds, then dropping down due to the horizontal folds.
I still can't rule out a leak somewhere near the top of the liner, but I'm hoping fixing those siphon points will solve the problem. This morning, I put a stick with a mark on it in the intake bay, filled it up to the mark...and now, we wait.