If you short the phases together (melted phase wires, burned insulation on phase windings, axle spinout from excessive torque twisting up the axle wires), or short phases to halls (melted phase/hall wires, twisted axle wires), then you can destroy FETs, gate drivers, and potentially the actual MCU in the controller.
The only protection you can add against that is not causing those kinds of failures, by not running the system too hard and overheating or overtorqueing things.
You can add multiple-point temperature monitoring, but you'll need to watch a bunch of thermometer displays all the time to see if any overheat, or use ones with alarms you can set, or monitor all the sensors with an arduino/etc and have it alarm you or even just shut off the controller on overheat.
Up to the point the axle itself breaks, you can prevent (mostly) axle spinout (and the wire damage that causes) by using clamping torque plates with or instead of dropouts on your frame. See The Torque Arm Picture Thread for some examples; others are scattered around the forum and less easy to find in a search.
The axle itself will break at some point past it's "ratings" (there usually are no torque ratings for those available from the manufacturers, so you can only guesstimate or test to destruction); it's hard to predict because most hubmotors are not designed very well, compounded by poor manufacturing and quality control of both materials and workmanship, so there can be hidden defects (cracks, casting flaws, etc) in teh axles and other parts, too.
