In my experience with ESPs (mostly Salesforce Marketing Cloud Email Studio/Exact Target) any click on an email is counted by default in the CTR. As others have mentioned, there is value in tracking total clicks where all clicks are created equal. However, of course know that there are some clicks you intend to drive (the main CTA) some that are good to get anyway (social shares, login into account, etc..), and 1 you dont want (unsubscribe). There is a way to see a breakdown of all clicks (in SFMC it's a Link Click Report) where you can tease out the clicks you want to see. If you can find this report in the ESP you're using you should be able to compare the standard CTR you're seeing vs the one you can calculate with the link click report.
At our agency we typically report out to clients both the CTR and the "Meaningful CTR" which is all clicks, except clicks on unsubscribe. Note: you can do that for both unique and cumulative CTR but we focus more on unique