I'm having this same problem as well, except for me it's just when I dock and undock the machine with the 3 in 1 adapter. Doesn't happen all the time, but maybe every other day, then I have to reset the machine or it stops registering my Apple usb keyboard through the usb-c adapter.
I have DP6 and a 2015 rMB. Exactly the same experience. I need to reboot to get the USB port to recognize devices. With the 3-in-1 adapter, VGA keeps working, though. Only USB port is affected.