The exact same thing has happened to me. My intention was to write a post and ask for advice on how to avoid this when I've found this thread. Seems like I'm not the only one with this problem. I had a perfectly working setup and successfully conducted a few motor tests. I use two Pololu 298:1 12V metal gear motors with a Pololu TB6612FNG breakout board and I power the system using a PDB (this one from Diatone). Arduino and TB6612FNG are fed from the 5V BEC and motors from 12V (through the motor driver's motor pins VMOT, obviously). I've purchased the motors and the driver from robotshop.com.
So I had this setup working fine and I was carrying it around in a plastic box. One day I wanted to install it on my robot when I discovered it's not driving the motors anymore. I double and triple checked the wiring, the solder joints and the Arduino code as well and tested pin outputs using my DMM. I've found that A01/A01/B01/B02 do not output anything and a bump has appeared on the chip. What could have happened to it and how to avoid this?