Shorting Single Board Computer

I just finished designing a SBC based on the SAM9X60D1G. I checked all of the power rails for shorts before powering the board up. However, when I did power the board up, the PMIC I am using, the MCP16501TA-E/RMB, started smoking. After that, there was a short between 5v and GND, and 3V3 and GND. When I tested for continuity the next day, these shorts had vanished. I tried physically cutting the GND connection that appear to be shorting, but that didn't do anything.