Precise English speakers would say, "The tree has only one leaf" to express the intended meaning. This makes "only" modify "one." This is logical but doesn't seem to reflect the Vietnamese grammar. In conversation, many (if not most) English speakers actually say, "... only has... " which isn't literally true because the tree obviously has roots, branches, etc., in addition to that leaf. I am, of course, nitpicking as far as conversational English is conncerned but, if we are talking about what is correct or what should be accepted, then, I think, logic and grammar have a place in the discussion.