Arduino giga board got burnt twice. Do not know the reason. Please help if anyone can !

Hi,
I was using Arduino giga board for one of my projects that I recently bought. In this project I was testing and modifying the circuit to work properly. However, suddenly out of no where the board stopped working and the ON LED was not lit anymore. I do not understand what went wrong. I am sure none of the ports were directly grounded and now the entire board is not woking. Please let me know could have gone wrong so that I can avoid those mistakes in future.

"suddenly out of no where the board stopped working" Which of the following rules did you violate?
Gil's Crispy Critter Rules:
Rule #1. A Power Supply the Arduino is NOT!
Rule #2. Never Connect Anything Inductive to an Arduino!
Rule #3 Connecting or disconnecting wires with power on.
Rule #4 when first starting out, add a 220R resistor in series with both Input and Output pins. (LarryD)
Rule #5 buy a DMM to measure voltages, currents and resistance. (LarryD)
Violating these rules tends to make crispy critters out of Arduinos.

Why did you think it was not opeating properly?

Schematic(s) please

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I needed it to generate a series of pulses with varying width. Sometimes the pulses were not in correct polarity.. in those cases I was changing the the wiring.

How were you changing the wiring?