"Botella" just happens to be spelled that way, and is therefore feminine. It will not change to match the grammatical gender of its contents. In other words, the masculine "vino" inside will not have any affect on "botella". :-)
Nouns will usually only change gender if they are in reference to people or animals:
- boss = jefe (masc.) / jefa (fem.)
- cat = gato (masc.) / gata (fem.)
Really good article about how the (my) native English tendency to say "i would like" or "can i have" when ordering doesn't work well in Spanish. I mean, it works, i've said "puedo tener..." many, manh times in spain, peru, etc, but its not how Spanish speakers talk, it seems. It's good to learn these verbs from duo and makes it easier on us learners if we can say what feels natural, but i'm unsure duo should offer them as the spanish phrase to be translated. I don't want them to call it incorrect, either...