Google's John Mueller said on Twitter that the Google Search Console search analytics report only tracks clicks as clicks when the user clicks on something in the search results that leads you directly to your web site.
So in the case of a phone number showing up in the search suggestions or search results and if the searcher clicks on that phone number, then that click won't be counted because it doesn't lead to the web site, but instead leads to your phone app and dials the number.
Such as in this example screen shot, the click on the phone number will dial that number and not go to any web page:
John wrote on Twitter:
Clicking it doesn't lead to the site, so no click counted.
— John ☆.o(≧▽≦)o.☆ (@JohnMu) March 6, 2018
Forum discussion at Twitter.
