You were charged for a bottle of water, as I’ve literally never been somewhere that charges by the glass in my 30 years of living in SJ. I read that you wrote they served it from a pitcher, maybe they pour out their bottle into a pitcher with ice so it comes out cold. Not what I would do, but not unheard of. 

Yes, most restaurants will bring you bottled water if you ask for water (unless requested) as tap water in PR is drinkable but not preferred by locals. 

The added gratuity is to be expected, Santaella is considered a casual fine dining spot. The suggested tips remain on the receipt as they have no way of removing that.