I'm running 2.1.2 but since 2.0.1 I'm facing the same problem.
I have a custom theme and when I created file "_theme.less" under my template's structure (web/css/source) all those icons based on fonts get smaller. I mean Cart, Heart (wish list) and Bars (to compare). The weird thing is that the problem persist even if this _theme.less file is totally empty. When I remove the file everything went back to normal (without my customs, of course)
My custom template has Luma as parent so I tried copying all Luma's fonts to my own folder, also copied Blanks fonts but didnt work:
myuser@server: app/design/frontend/CustomTemplates/MyTemplate/web/fonts# ls
Blank-Theme-Icons.eot Blank-Theme-Icons.ttf Blank-Theme-Icons.woff2 Luma-Icons.svg Luma-Icons.woff selection.json Blank-Theme-Icons.svg Blank-Theme-Icons.woff Luma-Icons.eot Luma-Icons.ttf Luma-Icons.woff2
I'm flushing the cache before testing.