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I doubt the cover is causing the issue, I would think it is more a problem with the material. You can repair the bubbles, it can be normal to develop a few bubbles and leaving them is fine however if you want to repair them it can be done, never poke or cut the bubbles this could lead to more problems with water entry.. Butyl rubber sealant is the most effective for filling bubbles. Disposable syringes should work fine. Inject some sealant into the bubble and disburse it evenly. Once you have the surface flattened putting something heavy over top of the surface will help adhere the area while it is drying. IF you have more questions or concerns please feel free to contact me..
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