The pinkish staining appears to be a bacterial growth which has caused the staining, the magenta (pinkish) colour is normally associated with a bacterial micro-organism.
Although the vinyl coating on a spa is treated to resist bacteria (meaning it is not a suitable food source), it is still a perfect host site for this particular micro-organism. Other than looking strange, staining should not affect the use of your cover or enjoyment of your spa.
The stains are extremely hard to remove, but are prevented by regular cleaning and drying particularly in areas such as stitching and seams. We would suggest using the following products; Miracle pads, Stain remover or washing up liquid with warm water.
Unfortunately, this is not a manufacturing defect and the Aftersales Team will not be able to replace this under warranty for you. Replacement covers can be purchased here.