If the fan was faulty it can draw excessive amount of amps which would melt the cable and put stress on your motherboard..... I would be looking at it, did the fan get hot as well, did it spin up to full / rated speed ?
How many amps does the fan draw.... How long is the extension cable ?
... Noctua NF-A14 rated at 0.55A connected to the fan extension card by the cable supplied with the fan.
I only ever had one defective Noctua fan in 15 years and it didn't spin what-so-ever from first use and got hot, still amp draw was never enough to melt anything. I can also say I have fans of theirs over 8 years still running 24/7.
I have taken a look at your manual and noticed this is the most likely problem, that the header your using, isn't correct one for fan input. See diagram below I suspect your using the wrong header.