Small clicks is not a normal characteristic of that lens. But, depending on your AF settings that could be normal.
The fact that you say it only happens when you use IS might indicate there is nothing wrong, especially if you are using AI Servo focusing. If the small clicks sound more soft scratching noises, as compared to a small tap, then you might be hearing the IS system adjusting AF motors as the system tracks whatever is under the active AF point.
If you are using One Shot focusing, it is normal to hear a quick purr of AF motors. But once again, the motors sound more like a whirring or scratching sound than a hard click, at least it does to my old ears.
If you are in doubt, contact Canon Support, and they can help you confirm or deny that there is an issue better than asking questions in the forum. We are all simply users here [actually camera geeks, IMHO]. We share our knowledge and experiences, and are not employed by Canon. Sometimes a Canon Forum Moderator might chime in on a post, when the community might get stuck on a question, but you can readily tell who they are by their signatures and avatars.
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