I have the same problem with my MacBook 12" Retina early 2015. It all started when I did an upgrade to either El Capitan 10.11.5, or an upgrade for the USB-C Digital AV Multipart Adapter. Can't be sure which one it was. But since, all USB 3.0 devices fail to be recognized by the computer, unless I restart or reboot it in some way.
I have tried several old USB (2.0) flash drives and an external drive (Passport) also 2.0 and all work fine all the time, but once I try to use the new 3.0 devices, I have the same problem.
Recently I re-installed El Capitan (same version) and now it's been working intermittently, some times the 3.0 devices will mount and some times they don't.
It's a real pain in the neck because now I can't rely on my 3.0 devices.
The USB-C is a new technology and when I bought the MacBook I accepted there were going to be some problems, now I regret trading my MacBook Air, maybe one of this days I will just do that.