You need to make sure the edge of the pond is higher than the surrounding land. You want any water to flow around the pond. With all the rain the water flowed behind the liner filled it up with water which pushed the pond liner in. You might have had a mini river from run off in the yard that found a low spot that started running under your liner.
To fix (are the dirt walls collapsed too) if no walls collapsed, you need to get the water out, either let it go back into the soil or pump out, the berm up the edge of your pond to keep water from flowing under the liner.
If the walls collapsed, the only way to fix, is to drain pull the liner out or forward from the walls, shovel out the dirt, rebuild your wall.
Sorry you are having these issues.
I have the dirt sloping back around our pond to send any serious rains away from the pond. Also dug pits in some places and filled the pits with gravel to collect water, like a french drain.
Like slakker says do you have an overflow, the pond may have over flowed and the water filled up behind the liner. I made our overflow where when it does overflow the water can not flow back and under the liner.