If you're using the in-camera mic, then yes... it'll always pick up the sound of focusing. This was part of the point of Canon's new STM lenses in that they are nearly silent. They aren't technically perfectly silent as if you listen carefully even those lenses can sometimes be heard focusing (though it is extremely quiet). The USM focus motors are fairly quiet, but much snappier to focus.
To avoid hearing the focus motor, it's best to use an external mic. Rode VideoMic series can mount in the hot-shoe (they don't use any electronics of the hot-shoe... they just use it as a mount point) will provide better audio quality while also isolating themselves from the sounds of the camera. They're probably the most popular mics used for DSLR video.
Tim Campbell
5D III, 5D IV, 60Da
