Animals, kids, gardeners and over-grown plants can move rocks so that they deflect water out of the pond or force the lip of the liner below the water level.
Punctured liner by animals (or golf shoes!). This is extremely rare and can be fixed easily with a patch kit from Sunland Water Gardens.
Overgrown plants in the stream or waterfall may cause water to rise above liner level, which will result in a loss of water. Just thin out the plants to allow the water level to return to normal.