Small wrinkles in a vinyl liner that were not there to begin with are usually caused by poor water balance. Acidic water will slowly remove plasticiser from a vinyl liner. This causes the liner to stretch and eventually causes wrinkles.
There is no way to replace the plasticiser, so the only way to remove the wrinkles is to replace the liner.
To prevent the problem, maintain proper water balance. The presence of stabiliser has also been shown to reduce wrinkling and deformation of vinyl liners.