We're starting to use netduino 2 for our devices too (as a universal digital I/O remoter) and I'll report what happened to us, in the spirit of global knowledge.
In our laboratory, during our custom developed shields test, one netduino 2 became fried. The technician that was making the tests inserted an external connector that carry 12V and 3.3V... inverted. So that 12V came in 3.3V pin of netduino. I don't know what happened at the moment but after that I've checked the board and, obviously, it's unresponsive, only white led turn on (not the blue one) and no communication in USB port. My PC don't see anything anymore, so MFDeploy and netduino update see nothing too (obviously). The ARM chip is becoming very hot when powered but no buzzing sounds. Simply... fried! (our fault, of course)
But now I have a wonderful paperweight