I believe everyone will read the sentence in question only as "I want to make an apple pie with apples". To say the other, you have to say or something like this. Japanese particles (as well as English prepositions) each have many meanings, and the context is often the only clue. You have to get used to them by examples. (For example, one of the meanings of "by" in English is "alongside/near", but "go to school by bus" never means going to school by running after a bus.)