MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
No idea, I'm a software guy, I do hobby electronics myself but circuit design is way over my head. This is definitely a known issue for Trigorilla boards, might just be missing some particular protection circuitry, but I really don't have a clue.
But we often underestimate what it takes to make a safe circuit design. I recently looked into safe PWM controlled hotbed circuits. Turns out reverse voltage is actually a big issue and most printer boards (e.g. RAMPS, Melzi, RUMBA) lack the freewheeling diode to mitigate that. It still works well for most because the MOSFETs are reasonably sized.
Anyways, the puny little J3Y transistor on FAN0 just loves to fry in those occasions, not much you can do. You won't have that issue anymore, replacing it with a proper one from Infineon, etc.