Hey Anne,
Thanks for writing in. We haven't had any other users reporting that their callto: or tel: links are showing up as relative links in their crawl diagnostics so I dug into the formatting a little bit. From the research I've done (http://demosthenes.info/blog/536/Adding-Phone-Numbers-To-Web-Pages-With-HTML5-and-Microdata), it seems that the links may be formatted incorrectly as they are missing the + symbol mentioned in the post before the number in the link. I also tried clicking the callto: link on the site from a mobile browser and the link was not handled correctly there either. Basically, nothing happened unless I held the link down and then my browser tried to open the page as a relative link, as well.
Since I am not a web dev, I can't really advise on the proper formatting for these links, so I think this would be a better question for the community as a whole. I am going to change the category of the question to Technical SEO Issues and Web Design, which will allow the community to advise the proper formatting for these types of links.
I hope this helps!
Chiaryn