I had a lot of such discussions with my supervisor. He knows the field much better than me, so I never thought he was mistaken on specific facts. Instead, most of our disagreements were on what the next steps would be.
S: Maybe you can improve the second step using [algorithm].
D: No, that is not going to work because [...the data is too complex...].
This usually started an engaging discussion on the details of the data, alternative algorithms, and ways to circumvent it altogether. For this to work, you have to listen carefully to what he says, have an open mind and learning attitude, be polite, and of course, keep the discussion on a purely scientific level. Your arguments should be supported by evidence, and it should be clear how strongly supported they are.
Also, I think you should indicate how convinced you are when you phrase it. This way you give a true idea of how confident you are, and how much thought should they put into your idea. Furthermore, if you confidently assert something that is factually wrong (and this doesn't happen too often), you get a better chance of getting a detailed and enlightening lecture on why it is wrong.