Hi,
There are many reasons.
1.While testing /manipulating power and ground could have shorted.(If there are connectors , berg stick & jumper with power and ground this may occur)
2.Maintaining Proper common grounding(i have damaged cyclone iv with same issues there was a minor shock which i was filling when i touch the spacers of my board it was working fine after 2 day it got vcc and gnd shorted than after debugging power path, we have removed FPGA and tested and we found FPGA was damaged)
3.Also it can be because of ESD.
Best Regards,
Anand Raj Shankar
(This message was posted on behalf of Intel Corporation)