Well, this one is pretty unusual. I was doing some hacking around with my 2012 Nexus 7, and I found a peculiar issue: the Android SDK fastboot tool is causing the Macbook Pro's internal keyboard and mouse to entirely stop responding. The keyboard light remains on and external USB peripherals work, but the internal ones refuse to and the mac refuses to go to sleep (something I used to do to remedy a similar issue with Yosemite.)
It seems to correspond to when the flash actually occurs, but not to whether or not it's successful. So if you attempt to flash, the bug occurs and the OS is toast. Maybe libusb related?