Raspberry pi3 12v led circuit - broke down pi
When those transistors are turned on, there's what amounts to a short circuit through the associated LED to ground. You need an appropriately sized resistor in series with those LEDs.

I suspect what happened (the failure mode you experienced) is that the transistors got damaged by overcurrent, and the failed transistor inadvertently fed 12V back into your GPIO pin and that baked your Pi.