3 Things at play here

It is illegal to bring your own products in to a cafe to be consumed. It has to do with vat being charged on goods that you will eat while inside the establishment. Some places even charge less for take away food compared to the eat in, the difference being the vat.

Even if the product is free and your own is exactly the same thing it can't be consumed because of this. He should have provided a glass of water not just the glass.

I am also sure a food safety rule comes into play about the establishment owner needing to provide details of the source of the products in the event something happens eg food poisoning and they can't do that if they don't provide everything.

And finally it will have to do with alcohol licencing as the establishment owner may not have a licence (probably not for a cafe) and what you had in the bottle could have been anything.