You shouldn't be getting a noise if your shifts are smooth. If you have too high or too low of rpms you will hear the sound of the engine trying to keep up with the transmission or the clutch skipping on the flywheel. Neither of those are good things to have happen to your transmission, engine, and their mounts. The only other possibility is that you are griding gears and that is way bad and you should know that sound. If it isn't because of that you probably should go in to the dealer or a mechanic and see if they can pinpoint the noise.