As stated in other PhantomSkinz threads, their screen protectors usually take a few days to "heal" properly. It's unfortunate, but otherwise they are awesome protectors.
Continue to "condition" the protector by rubbing it and/or using the application card. Multiple times a day will help. Eventually any remaining air pockets and water will be removed after a few days. Should be safe to run the device as long as any excess water is not present to drip into any cracks in the phone casing.
Just for future reference - water is not required.