The roots of a gunnera can definitely pierce a pond liner, you water is probably draining away underneath as the gunnera puts its roots down. Ideally a bog garden should have some movement of water through it as static water will become anaerobic.

the gunnera could certainly be the culprit. but at this time of year a warm couple of days will lead to a lot of surface evaporation and this would cause the water level to drop. do you have a circulation system for the fish? again that will aid evaporation.

what type of liner did you use? heavy duty butyl liner shouldn't have ruptured but some of the thinner ones would as mg says.