They can't fill your bottle because it's a health code issue, if the neck of their bottle comes in contact with yours it could cross contaminate. Since they don't provide small bottles it's how they need to do it. However if they have a partial bottle that could fully empty into yours they could (might) do it for you.
On a side note they won't give you a full can of soda without popping top, because it could be used as a blunt object if it were thrown. How sad is it that somebody either did that or came up with that idea. But it's how it is.