With a fairly new liner the wrinkles being confined to the shallow end floor points to something my boss calls 'surface water' (this is different from ground water in that it's the result of the winter snow meltoff and spring rains not being able to pass through the dirt surrounding the pool quickly enough so some 'puddles' at > the floor level while waiting to be absorbed which pushes the liner up-- ground water is what caused the deep end floating a few years ago, the water table in the pool area came up higher than the floor), if the yard or neighbor's yard slopes towards your pool, it's gonna keep happening until you can improve the drainage around the pool . I also assume that you have been keeping the pH > 7.0.

Back to the origional ?, which I overlooked in my first response , with a high water table, or drainage issues - keep as much water in the pool as you can when you close! You can use a blower (many types) to evacuate the water from the lines and plug them while the air is still being forced through them without having to fear ice damage (whoever does the plugging will get wet ). If you want to be able to keep the water at ~ opperational level, they make 'blow through' skimmer freeze protection Gizzmos. The morre water in the pool, the better the liner will be able to resist the ground or surface water!