Hello guys,
I'm running 2.1.0 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.
 
Any idea?
Thank you!